14-50690442-G-A

Position:

• chr14-50690442-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 0.746 in 151,906 control chromosomes in the GnomAD database, including 42,589 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 0.75 (42589 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 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: 0.746 AC: 113237 AN: 151788 Hom.: 42549 Cov.: 30

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.746 AC: 113334 AN: 151906 Hom.: 42589 Cov.: 30 AF XY: 0.748 AC XY: 55493 AN XY: 74234

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.727

Alfa AF: 0.703 Hom.: 75945

Bravo AF: 0.755

Asia WGS AF: 0.810 AC: 2794 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3015469; hg19: chr14-51157160;