5-4022536-G-A

Variant names:

• chr5-4022536-G-A
• rs490556

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 0.567 in 152,014 control chromosomes in the GnomAD database, including 25,433 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 0.57 (25433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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: 0.567 AC: 86054 AN: 151896 Hom.: 25405 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.567 AC: 86136 AN: 152014 Hom.: 25433 Cov.: 32 AF XY: 0.571 AC XY: 42446 AN XY: 74318

African (AFR) AF: 0.719 AC: 29794 AN: 41462

American (AMR) AF: 0.554 AC: 8473 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3466

East Asian (EAS) AF: 0.779 AC: 4002 AN: 5140

South Asian (SAS) AF: 0.590 AC: 2845 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5869 AN: 10572

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31436 AN: 67954

Other (OTH) AF: 0.555 AC: 1169 AN: 2108

Alfa AF: 0.388 Hom.: 1069

Bravo AF: 0.573

Asia WGS AF: 0.667 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.066
DANN	Benign	0.81
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs490556; hg19: chr5-4022650;