rs7143894

Positions:

• chr14-57171114-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 0.287 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;