rs11631682

Variant names:

• chr15-74764017-G-A
• rs11631682

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 0.0478 in 152,212 control chromosomes in the GnomAD database, including 251 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 0.048 (251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 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: 0.0478 AC: 7274 AN: 152094 Hom.: 251 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0423

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

GnomAD4 genome AF: 0.0478 AC: 7272 AN: 152212 Hom.: 251 Cov.: 32 AF XY: 0.0492 AC XY: 3665 AN XY: 74446

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0614

Gnomad4 EAS AF: 0.0727

Gnomad4 SAS AF: 0.0861

Gnomad4 FIN AF: 0.0373

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0418

Alfa AF: 0.0384 Hom.: 23

Bravo AF: 0.0479

Asia WGS AF: 0.0700 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631682; hg19: chr15-75056358;