rs2143956

Variant names:

• chr14-54381173-C-G
• rs2143956

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;