Question: missing the variant NM_000251.2(MSH2):c.942+3A>T in variant calling
gravatar for AshishKS
3.2 years ago by
AshishKS10 wrote:

A variant is not getting called at position in MSH2 gene at ch2:47641560 (c.942+3A>T) It is a known pathogenic mutation. ( ) and this variant have been mention in literature for not getting called ( ), they say that "located in the 3′ end of exon 5 in a difficult-to-sequence homopolymer stretch of 27 adenines" so, I am OK with the fact that my VC pipeline is not calling this variant in a specific sample. (though T being 42% and most of them passing the phread-quality score). We have verified this variant in the same sample through Sanger sequencing. below are attached 1st & 2nd Image, Purple:forward strand, green:reverse strand).

BUT....................... just next to this position at ch2:47641561 (c.942+4A>T), a variant is getting called for the same sample, though T is only 3% (4/121) at that position. below are attached 3rd & 4th Image, (purple:forward strand, green:reverse strand). I could not understand the reason... CAN ANYONE EXPLAIN IT??

1_forward 1_reverse 2_forward 2_reverse

Thanks & Happy Chrismas


sequencing snp next-gen • 810 views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by AshishKS10

It looks like a single base heterozygous deletion from the first screenshot rather than an A>T change.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Vivek2.4k

see 1st &2nd images (append) as one and 3rd and 4th as one (could not took sot of them in single frame) may be this story can help,


ADD REPLYlink written 3.2 years ago by AshishKS10
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