rs11637980

Variant names:

• chr15-96459423-A-G
• rs11637980

Your query was ambiguous. Multiple possible variants found:

• chr15-96459423-A-G
• chr15-96459423-A-T

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 0.173 in 152,100 control chromosomes in the GnomAD database, including 2,828 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 0.17 (2828 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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: 0.173 AC: 26343 AN: 151980 Hom.: 2822 Cov.: 33

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.173 AC: 26363 AN: 152100 Hom.: 2828 Cov.: 33 AF XY: 0.176 AC XY: 13081 AN XY: 74318

African (AFR) AF: 0.0479 AC: 1992 AN: 41544

American (AMR) AF: 0.188 AC: 2876 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5158

South Asian (SAS) AF: 0.271 AC: 1302 AN: 4810

European-Finnish (FIN) AF: 0.236 AC: 2487 AN: 10550

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14458 AN: 67966

Other (OTH) AF: 0.179 AC: 378 AN: 2114

Alfa AF: 0.195 Hom.: 5771

Bravo AF: 0.165

Asia WGS AF: 0.299 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs11637980; hg19: chr15-97002653; COSMIC: COSV58901734;