5-63694548-C-T

Variant names:

• chr5-63694548-C-T
• rs4527551
• ENST00000722712.1:n.391+3257G>A

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.391+3257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,874 control chromosomes in the GnomAD database, including 35,755 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 0.68 (35755 hom., cov: 32)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 0 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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.391+3257G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103441 AN: 151758 Hom.: 35738 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.682 AC: 103504 AN: 151874 Hom.: 35755 Cov.: 32 AF XY: 0.687 AC XY: 50997 AN XY: 74232

African (AFR) AF: 0.560 AC: 23210 AN: 41424

American (AMR) AF: 0.692 AC: 10554 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3468

East Asian (EAS) AF: 0.866 AC: 4481 AN: 5176

South Asian (SAS) AF: 0.777 AC: 3747 AN: 4824

European-Finnish (FIN) AF: 0.773 AC: 8138 AN: 10532

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48507 AN: 67878

Other (OTH) AF: 0.690 AC: 1458 AN: 2112

Alfa AF: 0.705 Hom.: 7827

Bravo AF: 0.671

Asia WGS AF: 0.812 AC: 2802 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.69
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4527551; hg19: chr5-62990375;