chr6-137101615-T-C

Variant names:

• chr6-137101615-T-C
• rs276568

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.565 in 150,266 control chromosomes in the GnomAD database, including 24,956 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24956 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.565 AC: 84804 AN: 150148 Hom.: 24940 Cov.: 25

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.570

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 84850 AN: 150266 Hom.: 24956 Cov.: 25 AF XY: 0.569 AC XY: 41695 AN XY: 73236

African (AFR) AF: 0.378 AC: 15426 AN: 40838

American (AMR) AF: 0.626 AC: 9458 AN: 15098

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1722 AN: 3466

East Asian (EAS) AF: 0.679 AC: 3438 AN: 5066

South Asian (SAS) AF: 0.625 AC: 2960 AN: 4734

European-Finnish (FIN) AF: 0.700 AC: 7071 AN: 10102

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 42821 AN: 67680

Other (OTH) AF: 0.568 AC: 1179 AN: 2076

Alfa AF: 0.611 Hom.: 57012

Bravo AF: 0.553

Asia WGS AF: 0.648 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		-0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs276568; hg19: chr6-137422752; COSMIC: COSV69427936;