5-63744946-A-G

Variant names:

• chr5-63744946-A-G
• rs7736910
• ENST00000722712.1:n.269-47019T>C

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.269-47019T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,890 control chromosomes in the GnomAD database, including 19,300 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 0.49 (19300 hom., cov: 32)
• Consequence: ENSG00000294317 ENST00000722712.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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.269-47019T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74794 AN: 151772 Hom.: 19288 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.493 AC: 74834 AN: 151890 Hom.: 19300 Cov.: 32 AF XY: 0.502 AC XY: 37230 AN XY: 74222

African (AFR) AF: 0.397 AC: 16463 AN: 41448

American (AMR) AF: 0.513 AC: 7834 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1938 AN: 3462

East Asian (EAS) AF: 0.840 AC: 4331 AN: 5154

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6459 AN: 10562

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33098 AN: 67880

Other (OTH) AF: 0.508 AC: 1069 AN: 2106

Alfa AF: 0.482 Hom.: 2174

Bravo AF: 0.480

Asia WGS AF: 0.738 AC: 2563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.83
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7736910; hg19: chr5-63040773;