rs4958525

Variant names:

• chr5-152290423-G-A
• rs4958525

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 0.133 in 152,118 control chromosomes in the GnomAD database, including 1,776 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 0.13 (1776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20196 AN: 151998 Hom.: 1779 Cov.: 32

Gnomad AFR AF: 0.0335

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0367

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.133 AC: 20179 AN: 152118 Hom.: 1776 Cov.: 32 AF XY: 0.133 AC XY: 9885 AN XY: 74354

African (AFR) AF: 0.0334 AC: 1387 AN: 41512

American (AMR) AF: 0.224 AC: 3423 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.0368 AC: 190 AN: 5166

South Asian (SAS) AF: 0.127 AC: 610 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1898 AN: 10572

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11696 AN: 67996

Other (OTH) AF: 0.133 AC: 282 AN: 2114

Alfa AF: 0.166 Hom.: 480

Bravo AF: 0.135

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.79
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4958525; hg19: chr5-151669984;