rs7143579

Variant names:

• chr14-54473967-C-A
• rs7143579

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,028 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.209 AC: 31718 AN: 151910 Hom.: 3995 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.209 AC: 31780 AN: 152028 Hom.: 4004 Cov.: 32 AF XY: 0.205 AC XY: 15204 AN XY: 74308

African (AFR) AF: 0.353 AC: 14637 AN: 41460

American (AMR) AF: 0.180 AC: 2751 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3468

East Asian (EAS) AF: 0.105 AC: 540 AN: 5160

South Asian (SAS) AF: 0.164 AC: 792 AN: 4816

European-Finnish (FIN) AF: 0.137 AC: 1450 AN: 10558

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10736 AN: 67960

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.171 Hom.: 1283

Bravo AF: 0.218

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.49
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7143579; hg19: chr14-54940685;