rs10792094

Positions:

• chr11-57394891-G-T

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 0.118 in 152,034 control chromosomes in the GnomAD database, including 1,188 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 0.12 (1188 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17955 AN: 151916 Hom.: 1188 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.118 AC: 17968 AN: 152034 Hom.: 1188 Cov.: 31 AF XY: 0.113 AC XY: 8435 AN XY: 74318

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.0505

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.0573

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.110

Alfa AF: 0.111 Hom.: 468

Bravo AF: 0.125

Asia WGS AF: 0.0920 AC: 321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10792094; hg19: chr11-57162364;