rs11231017

Positions:

• chr11-62293877-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 0.298 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.319

Alfa AF: 0.374 Hom.: 17216

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11231017; hg19: chr11-62061349;