rs632793

chr1-11850620-A-Gchr1-11850620-A-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 0.448 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

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 = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.426

Alfa AF: 0.407 Hom.: 5486

Bravo AF: 0.448

Asia WGS AF: 0.351 AC: 1222 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	3.5
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

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