rs1892953

Variant names:

• chr11-76561498-G-A
• rs1892953

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;