14-53925095-T-C

Position:

• chr14-53925095-T-C

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 0.707 in 151,732 control chromosomes in the GnomAD database, including 40,683 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 0.71 (40683 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107270 AN: 151616 Hom.: 40688 Cov.: 30

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.707 AC: 107280 AN: 151732 Hom.: 40683 Cov.: 30 AF XY: 0.706 AC XY: 52394 AN XY: 74160

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.728

Alfa AF: 0.811 Hom.: 23460

Bravo AF: 0.687

Asia WGS AF: 0.626 AC: 2178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498466; hg19: chr14-54391813;