rs1892953

chr11-76561498-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 0.564 in 151,966 control chromosomes in the GnomAD database, including 24,345 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 0.56 (24345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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: 0.564 AC: 85640 AN: 151848 Hom.: 24342 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.564 AC: 85680 AN: 151966 Hom.: 24345 Cov.: 32 AF XY: 0.560 AC XY: 41615 AN XY: 74280

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.571

Alfa AF: 0.577 Hom.: 12764

Bravo AF: 0.561

Asia WGS AF: 0.476 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.91
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1892953; hg19: chr11-76272542;