chr5-63740510-C-A

Variant names:

• chr5-63740510-C-A
• rs7714850
• ENST00000722712.1:n.269-42583G>T

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.269-42583G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 151,906 control chromosomes in the GnomAD database, including 39,089 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 0.71 (39089 hom., cov: 32)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 3 publications found

Genes affected

ENSG00000294317 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 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
ENSG00000294317	ENST00000722712.1	n.269-42583G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107714 AN: 151788 Hom.: 39042 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.710 AC: 107820 AN: 151906 Hom.: 39089 Cov.: 32 AF XY: 0.713 AC XY: 52942 AN XY: 74228

African (AFR) AF: 0.849 AC: 35202 AN: 41484

American (AMR) AF: 0.636 AC: 9683 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2126 AN: 3466

East Asian (EAS) AF: 0.835 AC: 4291 AN: 5142

South Asian (SAS) AF: 0.711 AC: 3420 AN: 4812

European-Finnish (FIN) AF: 0.745 AC: 7874 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43012 AN: 67902

Other (OTH) AF: 0.678 AC: 1428 AN: 2106

Alfa AF: 0.653 Hom.: 10041

Bravo AF: 0.707

Asia WGS AF: 0.782 AC: 2719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.17
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7714850; hg19: chr5-63036337;