rs11631403

Variant names:

• chr15-69156921-T-C
• rs11631403

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 0.705 in 152,178 control chromosomes in the GnomAD database, including 37,934 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 0.70 (37934 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.743 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: 0.705 AC: 107188 AN: 152060 Hom.: 37893 Cov.: 34

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.705 AC: 107275 AN: 152178 Hom.: 37934 Cov.: 34 AF XY: 0.704 AC XY: 52396 AN XY: 74388

African (AFR) AF: 0.685 AC: 28428 AN: 41514

American (AMR) AF: 0.755 AC: 11555 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3746 AN: 5170

South Asian (SAS) AF: 0.594 AC: 2866 AN: 4826

European-Finnish (FIN) AF: 0.705 AC: 7463 AN: 10590

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48564 AN: 67984

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.714 Hom.: 104222

Bravo AF: 0.713

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11631403; hg19: chr15-69449260;