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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.468 AC: 19380 AN: 41400

American (AMR) AF: 0.535 AC: 8164 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2384 AN: 3462

East Asian (EAS) AF: 0.533 AC: 2751 AN: 5158

South Asian (SAS) AF: 0.767 AC: 3696 AN: 4818

European-Finnish (FIN) AF: 0.596 AC: 6292 AN: 10550

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38665 AN: 67932

Other (OTH) AF: 0.583 AC: 1227 AN: 2106

Alfa AF: 0.534 Hom.: 2759

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
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs490434; hg19: chr4-46193279;