rs7143894

Variant names:

• chr14-57171114-C-T
• rs7143894

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 0.287 in 152,172 control chromosomes in the GnomAD database, including 13,434 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 0.29 (13434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 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: 0.287 AC: 43580 AN: 152054 Hom.: 13376 Cov.: 33

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0900

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.287 AC: 43693 AN: 152172 Hom.: 13434 Cov.: 33 AF XY: 0.275 AC XY: 20483 AN XY: 74398

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0901

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.241

Alfa AF: 0.139 Hom.: 4147

Bravo AF: 0.320

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
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: rs7143894; hg19: chr14-57637832;