ENST00000519819.5:n.72+20518T>C

Variant names:

• chr8-63440961-A-G
• rs1431587
• ENST00000519819.5:n.72+20518T>C

Variant summary

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

The ENST00000519819.5(ENSG00000253205):​n.72+20518T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,824 control chromosomes in the GnomAD database, including 45,352 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 0.77 (45352 hom., cov: 32)
• Consequence: ENSG00000253205 ENST00000519819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 3 publications found

Genes affected

ENSG00000253205 (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 = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375874	XR_001745932.2	n.429+3354A>G		intron_variant	Intron 1 of 3
LOC105375874	XR_001745933.2	n.429+3354A>G		intron_variant	Intron 1 of 2
LOC105375874	XR_928976.3	n.618+3354A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253205	ENST00000519819.5	n.72+20518T>C		intron_variant	Intron 1 of 2	3
ENSG00000253205	ENST00000521061.1	n.289-6952T>C		intron_variant	Intron 2 of 3	4
ENSG00000253205	ENST00000522265.6	n.286+20518T>C		intron_variant	Intron 2 of 6	4

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116538 AN: 151706 Hom.: 45298 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.768 AC: 116652 AN: 151824 Hom.: 45352 Cov.: 32 AF XY: 0.771 AC XY: 57212 AN XY: 74214

African (AFR) AF: 0.872 AC: 36148 AN: 41464

American (AMR) AF: 0.814 AC: 12401 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2293 AN: 3464

East Asian (EAS) AF: 0.938 AC: 4811 AN: 5128

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4824

European-Finnish (FIN) AF: 0.670 AC: 7081 AN: 10562

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47133 AN: 67836

Other (OTH) AF: 0.769 AC: 1625 AN: 2112

Alfa AF: 0.736 Hom.: 5350

Bravo AF: 0.784

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.76
DANN	Benign	0.66
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1431587; hg19: chr8-64353519;