chr14-25296377-C-T

Variant names:

• chr14-25296377-C-T
• rs974491

Variant summary

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

The variant allele was found at a frequency of 0.625 in 152,058 control chromosomes in the GnomAD database, including 29,853 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 0.63 (29853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 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: 0.625 AC: 94966 AN: 151940 Hom.: 29810 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.625 AC: 95057 AN: 152058 Hom.: 29853 Cov.: 32 AF XY: 0.628 AC XY: 46688 AN XY: 74312

African (AFR) AF: 0.602 AC: 24971 AN: 41468

American (AMR) AF: 0.594 AC: 9068 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1987 AN: 3472

East Asian (EAS) AF: 0.762 AC: 3940 AN: 5172

South Asian (SAS) AF: 0.687 AC: 3315 AN: 4822

European-Finnish (FIN) AF: 0.670 AC: 7083 AN: 10572

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42730 AN: 67968

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.627 Hom.: 18959

Bravo AF: 0.615

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.6
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs974491; hg19: chr14-25765583;