rs490556

Variant names:

• chr5-4022536-G-A
• rs490556

Your query was ambiguous. Multiple possible variants found:

• chr5-4022536-G-A
• chr5-4022536-G-C
• chr5-4022536-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 0.567 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.567 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

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.555

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490556; hg19: chr5-4022650;