rs490556

Positions:

• chr5-4022536-G-A
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;