rs269379

Variant names:

• chr3-19847774-G-A
• rs269379

Your query was ambiguous. Multiple possible variants found:

• chr3-19847774-G-A
• chr3-19847774-G-C
• chr3-19847774-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 0.445 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.444 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

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.383

Alfa AF: 0.354 Hom.: 2755

Bravo AF: 0.450

Asia WGS AF: 0.266 AC: 926 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs269379; hg19: chr3-19889266;