rs11231017

Variant names:

• chr11-62293877-G-A
• rs11231017

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 0.298 in 152,074 control chromosomes in the GnomAD database, including 7,903 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 0.30 (7903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 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: 0.299 AC: 45397 AN: 151956 Hom.: 7909 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.298 AC: 45394 AN: 152074 Hom.: 7903 Cov.: 32 AF XY: 0.300 AC XY: 22272 AN XY: 74352

African (AFR) AF: 0.112 AC: 4629 AN: 41510

American (AMR) AF: 0.295 AC: 4509 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1622 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1541 AN: 5166

South Asian (SAS) AF: 0.387 AC: 1863 AN: 4808

European-Finnish (FIN) AF: 0.385 AC: 4061 AN: 10560

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26084 AN: 67962

Other (OTH) AF: 0.319 AC: 672 AN: 2106

Alfa AF: 0.354 Hom.: 27433

Bravo AF: 0.284

Asia WGS AF: 0.352 AC: 1221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.086
DANN	Benign	0.27
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11231017; hg19: chr11-62061349;