14-53925095-T-C

Variant names:

• chr14-53925095-T-C
• rs10498466
• ENST00000729148.1:n.188-8183A>G

Variant summary

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

The ENST00000729148.1(ENSG00000295303):​n.188-8183A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,732 control chromosomes in the GnomAD database, including 40,683 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 0.71 (40683 hom., cov: 30)
• Consequence: ENSG00000295303 ENST00000729148.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 6 publications found

Genes affected

ENSG00000295303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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
ENSG00000295303	ENST00000729148.1	n.188-8183A>G		intron_variant	Intron 1 of 4
ENSG00000295303	ENST00000729149.1	n.141-8183A>G		intron_variant	Intron 1 of 3
ENSG00000295303	ENST00000729150.1	n.138-8183A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107270 AN: 151616 Hom.: 40688 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.707 AC: 107280 AN: 151732 Hom.: 40683 Cov.: 30 AF XY: 0.706 AC XY: 52394 AN XY: 74160

African (AFR) AF: 0.419 AC: 17262 AN: 41200

American (AMR) AF: 0.742 AC: 11314 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2801 AN: 5150

South Asian (SAS) AF: 0.722 AC: 3474 AN: 4810

European-Finnish (FIN) AF: 0.821 AC: 8663 AN: 10556

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58394 AN: 67986

Other (OTH) AF: 0.728 AC: 1536 AN: 2110

Alfa AF: 0.815 Hom.: 32351

Bravo AF: 0.687

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.80
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10498466; hg19: chr14-54391813;