rs11631682

chr15-74764017-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;