3-191826138-G-T

Variant names:

• chr3-191826138-G-T
• rs779279
• ENST00000820044.1:n.253+4708C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000820044.1(ENSG00000306673):​n.253+4708C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000306673 ENST00000820044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 1 publications found

Genes affected

ENSG00000306673 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820044.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306673	ENST00000820044.1		n.253+4708C>A		intron	N/A

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

African (AFR) AF: 0.284 AC: 11744 AN: 41382

American (AMR) AF: 0.424 AC: 6453 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1710 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4816

European-Finnish (FIN) AF: 0.556 AC: 5858 AN: 10540

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30530 AN: 67848

Other (OTH) AF: 0.390 AC: 821 AN: 2104

Alfa AF: 0.440 Hom.: 8760

Bravo AF: 0.388

Asia WGS AF: 0.399 AC: 1386 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs779279; hg19: chr3-191543927;