rs3213403

Variant names:

• chr19-43542576-T-C
• rs3213403

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 0.074 in 152,274 control chromosomes in the GnomAD database, including 629 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 0.074 (629 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.21
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11273 AN: 152156 Hom.: 629 Cov.: 31

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0619

Gnomad OTH AF: 0.0870

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

GnomAD4 genome AF: 0.0740 AC: 11274 AN: 152274 Hom.: 629 Cov.: 31 AF XY: 0.0746 AC XY: 5556 AN XY: 74460

African (AFR) AF: 0.0647 AC: 2688 AN: 41556

American (AMR) AF: 0.102 AC: 1558 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1486 AN: 5184

South Asian (SAS) AF: 0.104 AC: 502 AN: 4826

European-Finnish (FIN) AF: 0.0368 AC: 391 AN: 10618

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4206 AN: 68006

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.0690 Hom.: 1472

Bravo AF: 0.0810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.059
DANN	Benign	0.50
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs3213403; hg19: chr19-44046728;