14-25271769-T-C

Variant names:

• chr14-25271769-T-C
• rs1531023
• ENST00000837960.1:n.380-7254T>C

Variant summary

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

The ENST00000837960.1(ENSG00000309034):​n.380-7254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,922 control chromosomes in the GnomAD database, including 16,516 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 0.47 (16516 hom., cov: 32)
• Consequence: ENSG00000309034 ENST00000837960.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 3 publications found

Genes affected

ENSG00000309034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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
ENSG00000309034	ENST00000837960.1	n.380-7254T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70721 AN: 151804 Hom.: 16488 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.466 AC: 70792 AN: 151922 Hom.: 16516 Cov.: 32 AF XY: 0.468 AC XY: 34768 AN XY: 74252

African (AFR) AF: 0.452 AC: 18725 AN: 41440

American (AMR) AF: 0.463 AC: 7079 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2563 AN: 5160

South Asian (SAS) AF: 0.485 AC: 2336 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5185 AN: 10570

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32007 AN: 67882

Other (OTH) AF: 0.470 AC: 990 AN: 2108

Alfa AF: 0.465 Hom.: 6076

Bravo AF: 0.463

Asia WGS AF: 0.497 AC: 1723 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1531023; hg19: chr14-25740975;