chr14-26342515-C-T

Position:

• chr14-26342515-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.26342515C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;