rs2143956

Positions:

• chr14-54381173-C-G
• chr14-54381173-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 0.496 in 151,866 control chromosomes in the GnomAD database, including 19,641 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 0.50 (19641 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75330 AN: 151748 Hom.: 19627 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.496 AC: 75380 AN: 151866 Hom.: 19641 Cov.: 31 AF XY: 0.493 AC XY: 36568 AN XY: 74164

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.538

Alfa AF: 0.412 Hom.: 1243

Bravo AF: 0.489

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143956; hg19: chr14-54847891;