rs2652485

Variant names:

• chr5-5858697-C-A
• rs2652485

Your query was ambiguous. Multiple possible variants found:

• chr5-5858697-C-A
• chr5-5858697-C-G
• chr5-5858697-C-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 0.674 in 151,980 control chromosomes in the GnomAD database, including 35,355 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 0.67 (35355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.674 AC: 102306 AN: 151862 Hom.: 35308 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.674 AC: 102403 AN: 151980 Hom.: 35355 Cov.: 31 AF XY: 0.667 AC XY: 49552 AN XY: 74262

African (AFR) AF: 0.803 AC: 33304 AN: 41464

American (AMR) AF: 0.527 AC: 8028 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3468

East Asian (EAS) AF: 0.603 AC: 3107 AN: 5150

South Asian (SAS) AF: 0.475 AC: 2288 AN: 4812

European-Finnish (FIN) AF: 0.696 AC: 7347 AN: 10550

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44382 AN: 67978

Other (OTH) AF: 0.656 AC: 1384 AN: 2110

Alfa AF: 0.676 Hom.: 4548

Bravo AF: 0.668

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.85
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2652485; hg19: chr5-5858810;