rs11071746

Variant names:

• chr15-63441064-T-C
• rs11071746

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 0.707 in 151,940 control chromosomes in the GnomAD database, including 39,057 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 0.71 (39057 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.707 AC: 107367 AN: 151822 Hom.: 39032 Cov.: 30

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.707 AC: 107433 AN: 151940 Hom.: 39057 Cov.: 30 AF XY: 0.698 AC XY: 51837 AN XY: 74258

African (AFR) AF: 0.727 AC: 30116 AN: 41438

American (AMR) AF: 0.559 AC: 8530 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2839 AN: 3472

East Asian (EAS) AF: 0.244 AC: 1254 AN: 5146

South Asian (SAS) AF: 0.584 AC: 2811 AN: 4810

European-Finnish (FIN) AF: 0.715 AC: 7546 AN: 10556

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51794 AN: 67946

Other (OTH) AF: 0.728 AC: 1534 AN: 2106

Alfa AF: 0.740 Hom.: 143064

Bravo AF: 0.693

Asia WGS AF: 0.422 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.20
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11071746; hg19: chr15-63733263;