rs11071657

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;