rs7142517

Variant names:

• chr14-54840086-C-A
• rs7142517

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 0.244 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.257

Alfa AF: 0.279 Hom.: 636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7142517; hg19: chr14-55306804;