rs310501

Variant names:

• chr5-83594091-G-A
• rs310501

Your query was ambiguous. Multiple possible variants found:

• chr5-83594091-G-A
• chr5-83594091-G-C
• chr5-83594091-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 0.662 in 151,996 control chromosomes in the GnomAD database, including 33,618 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 0.66 (33618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 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: 0.662 AC: 100612 AN: 151878 Hom.: 33600 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.662 AC: 100679 AN: 151996 Hom.: 33618 Cov.: 32 AF XY: 0.668 AC XY: 49598 AN XY: 74302

African (AFR) AF: 0.584 AC: 24197 AN: 41428

American (AMR) AF: 0.727 AC: 11099 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2430 AN: 3466

East Asian (EAS) AF: 0.754 AC: 3896 AN: 5170

South Asian (SAS) AF: 0.845 AC: 4075 AN: 4822

European-Finnish (FIN) AF: 0.643 AC: 6785 AN: 10548

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45764 AN: 67980

Other (OTH) AF: 0.692 AC: 1458 AN: 2108

Alfa AF: 0.676 Hom.: 160989

Bravo AF: 0.661

Asia WGS AF: 0.791 AC: 2746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs310501; hg19: chr5-82889910; COSMIC: COSV60160820;