rs831791

Variant names:

• chr5-57053936-G-A
• rs831791

Your query was ambiguous. Multiple possible variants found:

• chr5-57053936-G-A
• chr5-57053936-G-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 0.506 in 151,994 control chromosomes in the GnomAD database, including 20,107 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 0.51 (20107 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.506 AC: 76804 AN: 151876 Hom.: 20107 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.506 AC: 76836 AN: 151994 Hom.: 20107 Cov.: 32 AF XY: 0.504 AC XY: 37417 AN XY: 74304

African (AFR) AF: 0.413 AC: 17103 AN: 41440

American (AMR) AF: 0.534 AC: 8139 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.188 AC: 972 AN: 5168

South Asian (SAS) AF: 0.494 AC: 2383 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5664 AN: 10552

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38685 AN: 67974

Other (OTH) AF: 0.517 AC: 1091 AN: 2112

Alfa AF: 0.547 Hom.: 12712

Bravo AF: 0.495

Asia WGS AF: 0.354 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.34
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs831791; hg19: chr5-56349763;