rs10791979

Positions:

• chr11-56392494-A-C

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 0.32 in 151,888 control chromosomes in the GnomAD database, including 8,975 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 0.32 (8975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.504 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: 0.320 AC: 48624 AN: 151770 Hom.: 8965 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.320 AC: 48671 AN: 151888 Hom.: 8975 Cov.: 32 AF XY: 0.312 AC XY: 23138 AN XY: 74246

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.303

Alfa AF: 0.294 Hom.: 1230

Bravo AF: 0.332

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10791979; hg19: chr11-56159970;