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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.350

Alfa AF: 0.366 Hom.: 17425

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11071657; hg19: chr15-62433962;