2-64313293-G-T

Variant names:

• chr2-64313293-G-T
• rs890478
• ENST00000717283.1:n.255-10449G>T

Variant summary

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

The ENST00000717283.1(ENSG00000288932):​n.255-10449G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 148,428 control chromosomes in the GnomAD database, including 21,540 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 0.54 (21540 hom., cov: 25)
• Consequence: ENSG00000288932 ENST00000717283.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 5 publications found

Genes affected

ENSG00000288932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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
ENSG00000288932	ENST00000717283.1	n.255-10449G>T		intron_variant	Intron 2 of 3
ENSG00000293670	ENST00000717288.1	n.264-10449G>T		intron_variant	Intron 1 of 2
ENSG00000293670	ENST00000717289.1	n.264-10449G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 79543 AN: 148324 Hom.: 21518 Cov.: 25

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.536 AC: 79603 AN: 148428 Hom.: 21540 Cov.: 25 AF XY: 0.538 AC XY: 38882 AN XY: 72214

African (AFR) AF: 0.605 AC: 24432 AN: 40386

American (AMR) AF: 0.478 AC: 7003 AN: 14646

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1720 AN: 3442

East Asian (EAS) AF: 0.240 AC: 1133 AN: 4724

South Asian (SAS) AF: 0.552 AC: 2576 AN: 4666

European-Finnish (FIN) AF: 0.594 AC: 5911 AN: 9954

Middle Eastern (MID) AF: 0.483 AC: 138 AN: 286

European-Non Finnish (NFE) AF: 0.521 AC: 35102 AN: 67388

Other (OTH) AF: 0.488 AC: 991 AN: 2030

Alfa AF: 0.506 Hom.: 9341

Bravo AF: 0.522

Asia WGS AF: 0.389 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.63
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs890478; hg19: chr2-64540427;