rs7142517

Variant names:

• chr14-54840086-C-A
• rs7142517

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 0.244 in 151,956 control chromosomes in the GnomAD database, including 5,553 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 0.24 (5553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.244 AC: 37078 AN: 151838 Hom.: 5558 Cov.: 31

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.244 AC: 37080 AN: 151956 Hom.: 5553 Cov.: 31 AF XY: 0.238 AC XY: 17654 AN XY: 74244

African (AFR) AF: 0.0797 AC: 3306 AN: 41470

American (AMR) AF: 0.223 AC: 3406 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1490 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5174

South Asian (SAS) AF: 0.241 AC: 1156 AN: 4804

European-Finnish (FIN) AF: 0.222 AC: 2343 AN: 10550

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23199 AN: 67922

Other (OTH) AF: 0.257 AC: 541 AN: 2106

Alfa AF: 0.310 Hom.: 9820

Bravo AF: 0.239

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.75
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7142517; hg19: chr14-55306804;