rs10791979

Variant names:

• chr11-56392494-A-C
• rs10791979

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.510 AC: 21126 AN: 41434

American (AMR) AF: 0.213 AC: 3250 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1242 AN: 3464

East Asian (EAS) AF: 0.133 AC: 688 AN: 5158

South Asian (SAS) AF: 0.194 AC: 935 AN: 4824

European-Finnish (FIN) AF: 0.193 AC: 2042 AN: 10574

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18351 AN: 67876

Other (OTH) AF: 0.303 AC: 636 AN: 2102

Alfa AF: 0.301 Hom.: 1339

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
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10791979; hg19: chr11-56159970;