14-25271769-T-C

Variant names:

• chr14-25271769-T-C
• rs1531023

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.470

Alfa AF: 0.461 Hom.: 3343

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531023; hg19: chr14-25740975;