5-63689606-G-A

Variant names:

• chr5-63689606-G-A
• rs1158292
• ENST00000722712.1:n.391+8199C>T

Variant summary

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

The ENST00000722712.1(ENSG00000294317):​n.391+8199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,892 control chromosomes in the GnomAD database, including 7,291 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 0.28 (7291 hom., cov: 31)
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986416	XR_001742672.2	n.382+673C>T		intron_variant	Intron 1 of 1
LOC107986416	XR_001742673.2	n.382+673C>T		intron_variant	Intron 1 of 2
LOC107986416	XR_001742674.2	n.382+673C>T		intron_variant	Intron 1 of 2
LOC107986416	XR_001742675.2	n.382+673C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294317	ENST00000722712.1	n.391+8199C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43102 AN: 151774 Hom.: 7291 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.284 AC: 43104 AN: 151892 Hom.: 7291 Cov.: 31 AF XY: 0.292 AC XY: 21654 AN XY: 74234

African (AFR) AF: 0.104 AC: 4316 AN: 41446

American (AMR) AF: 0.333 AC: 5077 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 911 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2490 AN: 5108

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4816

European-Finnish (FIN) AF: 0.445 AC: 4695 AN: 10544

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22817 AN: 67948

Other (OTH) AF: 0.287 AC: 606 AN: 2108

Alfa AF: 0.242 Hom.: 1179

Bravo AF: 0.267

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1158292; hg19: chr5-62985433;