3-191826138-G-T

Variant names:

• chr3-191826138-G-T
• rs779279

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 0.404 in 151,764 control chromosomes in the GnomAD database, including 13,043 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 0.40 (13043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 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: 0.404 AC: 61261 AN: 151646 Hom.: 13032 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.404 AC: 61295 AN: 151764 Hom.: 13043 Cov.: 32 AF XY: 0.411 AC XY: 30473 AN XY: 74160

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.390

Alfa AF: 0.441 Hom.: 7959

Bravo AF: 0.388

Asia WGS AF: 0.399 AC: 1386 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs779279; hg19: chr3-191543927;