rs4982958

Variant names:

• chr14-24518659-C-T
• rs4982958

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 0.502 in 151,856 control chromosomes in the GnomAD database, including 20,430 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 0.50 (20430 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 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: 0.503 AC: 76254 AN: 151738 Hom.: 20423 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.502 AC: 76277 AN: 151856 Hom.: 20430 Cov.: 31 AF XY: 0.497 AC XY: 36842 AN XY: 74182

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.495

Alfa AF: 0.582 Hom.: 12477

Bravo AF: 0.477

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4982958; hg19: chr14-24987865;