rs632793

Variant names:

• chr1-11850620-A-G
• rs632793

Your query was ambiguous. Multiple possible variants found:

• chr1-11850620-A-G
• chr1-11850620-A-T

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 0.448 in 152,074 control chromosomes in the GnomAD database, including 16,711 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 0.45 (16711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.646 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: 0.448 AC: 68012 AN: 151956 Hom.: 16675 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.448 AC: 68091 AN: 152074 Hom.: 16711 Cov.: 32 AF XY: 0.443 AC XY: 32929 AN XY: 74352

African (AFR) AF: 0.653 AC: 27051 AN: 41446

American (AMR) AF: 0.295 AC: 4506 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3472

East Asian (EAS) AF: 0.173 AC: 899 AN: 5182

South Asian (SAS) AF: 0.468 AC: 2252 AN: 4808

European-Finnish (FIN) AF: 0.360 AC: 3818 AN: 10592

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26912 AN: 67978

Other (OTH) AF: 0.426 AC: 898 AN: 2110

Alfa AF: 0.410 Hom.: 8375

Bravo AF: 0.448

Asia WGS AF: 0.351 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.61
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs632793; hg19: chr1-11910677; COSMIC: COSV64693597;