rs11071657

Variant names:

• chr15-62141763-A-G
• rs11071657

Your query was ambiguous. Multiple possible variants found:

• chr15-62141763-A-G
• chr15-62141763-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 0.31 in 152,046 control chromosomes in the GnomAD database, including 8,333 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 0.31 (8333 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 87 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.468 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: 0.310 AC: 47129 AN: 151928 Hom.: 8316 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.310 AC: 47162 AN: 152046 Hom.: 8333 Cov.: 31 AF XY: 0.310 AC XY: 23059 AN XY: 74314

African (AFR) AF: 0.135 AC: 5586 AN: 41502

American (AMR) AF: 0.477 AC: 7277 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.338 AC: 1752 AN: 5178

South Asian (SAS) AF: 0.299 AC: 1437 AN: 4812

European-Finnish (FIN) AF: 0.323 AC: 3408 AN: 10538

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25388 AN: 67968

Other (OTH) AF: 0.350 AC: 739 AN: 2110

Alfa AF: 0.356 Hom.: 39078

Bravo AF: 0.315

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11071657; hg19: chr15-62433962;