chr3-19847774-G-A

Variant names:

• chr3-19847774-G-A
• rs269379

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 0.445 in 151,728 control chromosomes in the GnomAD database, including 16,821 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 0.44 (16821 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.444 AC: 67373 AN: 151614 Hom.: 16791 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.445 AC: 67447 AN: 151728 Hom.: 16821 Cov.: 31 AF XY: 0.438 AC XY: 32499 AN XY: 74156

African (AFR) AF: 0.681 AC: 28182 AN: 41390

American (AMR) AF: 0.350 AC: 5328 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3466

East Asian (EAS) AF: 0.105 AC: 542 AN: 5166

South Asian (SAS) AF: 0.356 AC: 1709 AN: 4802

European-Finnish (FIN) AF: 0.332 AC: 3480 AN: 10474

Middle Eastern (MID) AF: 0.393 AC: 114 AN: 290

European-Non Finnish (NFE) AF: 0.382 AC: 25938 AN: 67882

Other (OTH) AF: 0.383 AC: 808 AN: 2108

Alfa AF: 0.373 Hom.: 3465

Bravo AF: 0.450

Asia WGS AF: 0.266 AC: 926 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs269379; hg19: chr3-19889266;