rs1953358

chr14-55828862-G-A

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 0.466 in 152,044 control chromosomes in the GnomAD database, including 16,904 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 0.47 (16904 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70812 AN: 151926 Hom.: 16886 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.466 AC: 70861 AN: 152044 Hom.: 16904 Cov.: 33 AF XY: 0.465 AC XY: 34545 AN XY: 74294

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.458

Alfa AF: 0.492 Hom.: 34740

Bravo AF: 0.472

Asia WGS AF: 0.537 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953358; hg19: chr14-56295580;