14-26342515-C-T

Variant names:

• chr14-26342515-C-T
• rs1950874

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 0.749 in 152,016 control chromosomes in the GnomAD database, including 45,327 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 0.75 (45327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.749 AC: 113824 AN: 151898 Hom.: 45331 Cov.: 33

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.749 AC: 113851 AN: 152016 Hom.: 45327 Cov.: 33 AF XY: 0.755 AC XY: 56083 AN XY: 74314

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.770

Alfa AF: 0.799 Hom.: 6243

Bravo AF: 0.720

Asia WGS AF: 0.851 AC: 2934 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1950874; hg19: chr14-26811721;