14-26342515-C-T

Variant names:

• chr14-26342515-C-T
• rs1950874

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 0.749 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.459 AC: 19031 AN: 41434

American (AMR) AF: 0.726 AC: 11103 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2935 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4787 AN: 5184

South Asian (SAS) AF: 0.885 AC: 4269 AN: 4822

European-Finnish (FIN) AF: 0.913 AC: 9621 AN: 10542

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59555 AN: 67956

Other (OTH) AF: 0.770 AC: 1628 AN: 2114

Alfa AF: 0.787 Hom.: 6327

Bravo AF: 0.720

Asia WGS AF: 0.851 AC: 2934 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.33
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1950874; hg19: chr14-26811721;