rs490434

Variant names:

• chr4-46191262-A-G
• rs490434

Your query was ambiguous. Multiple possible variants found:

• chr4-46191262-A-G
• chr4-46191262-A-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 0.548 in 151,888 control chromosomes in the GnomAD database, including 23,225 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 0.55 (23225 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.746 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: 0.548 AC: 83130 AN: 151770 Hom.: 23205 Cov.: 31

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.548 AC: 83190 AN: 151888 Hom.: 23225 Cov.: 31 AF XY: 0.552 AC XY: 40927 AN XY: 74198

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.583

Alfa AF: 0.537 Hom.: 2671

Bravo AF: 0.534

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.0
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490434; hg19: chr4-46193279;