chr5-63744413-G-A

Variant names:

• chr5-63744413-G-A
• rs13361996
• ENST00000722712.1:n.269-46486C>T

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.269-46486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 151,934 control chromosomes in the GnomAD database, including 765 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 0.088 (765 hom., cov: 32)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 2 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722712.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294317	ENST00000722712.1		n.269-46486C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13356 AN: 151816 Hom.: 767 Cov.: 32

Gnomad AFR AF: 0.0261

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0879 AC: 13354 AN: 151934 Hom.: 765 Cov.: 32 AF XY: 0.0852 AC XY: 6330 AN XY: 74254

African (AFR) AF: 0.0260 AC: 1080 AN: 41470

American (AMR) AF: 0.0902 AC: 1375 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5166

South Asian (SAS) AF: 0.0606 AC: 291 AN: 4800

European-Finnish (FIN) AF: 0.0897 AC: 947 AN: 10552

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8821 AN: 67910

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.0982 Hom.: 122

Bravo AF: 0.0876

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.7
DANN	Benign	0.83
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs13361996; hg19: chr5-63040240;