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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.692

Alfa AF: 0.682 Hom.: 80995

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

Splicing

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

Publications

LitVar

Other links and lift over

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