rs12639288

Variant names:

• chr3-167943348-G-A
• rs12639288
• ENST00000651627.1:n.46-2993C>T

Variant summary

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

The ENST00000651627.1(ENSG00000244706):​n.46-2993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,844 control chromosomes in the GnomAD database, including 4,960 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 0.24 (4960 hom., cov: 31)
• Consequence: ENSG00000244706 ENST00000651627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 8 publications found

Genes affected

ENSG00000244706 (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 = 0.308 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
ENSG00000244706	ENST00000651627.1	n.46-2993C>T		intron_variant	Intron 1 of 10
ENSG00000244706	ENST00000751769.1	n.132-15940C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35978 AN: 151726 Hom.: 4960 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.237 AC: 35988 AN: 151844 Hom.: 4960 Cov.: 31 AF XY: 0.236 AC XY: 17481 AN XY: 74198

African (AFR) AF: 0.128 AC: 5319 AN: 41470

American (AMR) AF: 0.175 AC: 2658 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3468

East Asian (EAS) AF: 0.0509 AC: 262 AN: 5144

South Asian (SAS) AF: 0.178 AC: 855 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3811 AN: 10522

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21163 AN: 67902

Other (OTH) AF: 0.237 AC: 499 AN: 2108

Alfa AF: 0.272 Hom.: 8642

Bravo AF: 0.218

Asia WGS AF: 0.124 AC: 431 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12639288; hg19: chr3-167661136;