rs11071746

chr15-63441064-T-C

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 0.707 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.728

Alfa AF: 0.745 Hom.: 97579

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11071746; hg19: chr15-63733263;