rs1958399

Variant names:

• chr14-20965183-T-C
• rs1958399

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 0.719 in 152,156 control chromosomes in the GnomAD database, including 39,539 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 0.72 (39539 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

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 (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.719 AC: 109273 AN: 152038 Hom.: 39502 Cov.: 33

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.719 AC: 109365 AN: 152156 Hom.: 39539 Cov.: 33 AF XY: 0.726 AC XY: 54002 AN XY: 74386

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.706

Alfa AF: 0.711 Hom.: 27652

Bravo AF: 0.718

Asia WGS AF: 0.811 AC: 2819 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	7.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958399; hg19: chr14-21433342;