rs11631292

Variant names:

• chr15-32745434-C-T
• rs11631292

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0609 in 152,264 control chromosomes in the GnomAD database, including 421 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 0.061 (421 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0803 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: 0.0610 AC: 9283 AN: 152146 Hom.: 421 Cov.: 31

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0411

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0609 AC: 9280 AN: 152264 Hom.: 421 Cov.: 31 AF XY: 0.0626 AC XY: 4664 AN XY: 74446

African (AFR) AF: 0.0144 AC: 600 AN: 41570

American (AMR) AF: 0.0600 AC: 918 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 308 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0408 AC: 196 AN: 4808

European-Finnish (FIN) AF: 0.124 AC: 1319 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0821 AC: 5584 AN: 68022

Other (OTH) AF: 0.0643 AC: 136 AN: 2116

Alfa AF: 0.0681 Hom.: 284

Bravo AF: 0.0545

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	8.9
DANN	Benign	0.64
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11631292; hg19: chr15-33037635;