3-4989276-C-T

Variant names:

• chr3-4989276-C-T
• rs2137947
• ENST00000814586.1:n.341G>A

Variant summary

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

The ENST00000814586.1(ENSG00000305983):​n.341G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,048 control chromosomes in the GnomAD database, including 34,422 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 0.64 (34422 hom., cov: 32)
• Consequence: ENSG00000305983 ENST00000814586.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677
• Publications: 11 publications found

Genes affected

ENSG00000305983 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814586.1. 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
	ENSG00000305983	ENST00000814586.1		n.341G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000305983	ENST00000814585.1		n.473-4964G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97780 AN: 151928 Hom.: 34407 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.643 AC: 97821 AN: 152048 Hom.: 34422 Cov.: 32 AF XY: 0.646 AC XY: 48011 AN XY: 74334

African (AFR) AF: 0.333 AC: 13807 AN: 41448

American (AMR) AF: 0.723 AC: 11062 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2691 AN: 3472

East Asian (EAS) AF: 0.660 AC: 3413 AN: 5168

South Asian (SAS) AF: 0.665 AC: 3167 AN: 4762

European-Finnish (FIN) AF: 0.787 AC: 8323 AN: 10582

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52884 AN: 68010

Other (OTH) AF: 0.676 AC: 1430 AN: 2114

Alfa AF: 0.734 Hom.: 76849

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.77
PhyloP100		-0.68

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2137947;

hg19: chr3-5030961;