rs10793396

Variant names:

• chr11-79811587-T-A
• rs10793396

Your query was ambiguous. Multiple possible variants found:

• chr11-79811587-T-A
• chr11-79811587-T-C

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 0.43 in 152,014 control chromosomes in the GnomAD database, including 14,725 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 0.43 (14725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65387 AN: 151898 Hom.: 14728 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.430 AC: 65410 AN: 152014 Hom.: 14725 Cov.: 32 AF XY: 0.437 AC XY: 32492 AN XY: 74284

African (AFR) AF: 0.304 AC: 12612 AN: 41462

American (AMR) AF: 0.498 AC: 7608 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2114 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2341 AN: 5142

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5872 AN: 10568

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31071 AN: 67974

Other (OTH) AF: 0.453 AC: 957 AN: 2114

Alfa AF: 0.445 Hom.: 1893

Bravo AF: 0.420

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.7
DANN	Benign	0.65
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10793396; hg19: chr11-79522631;