chr14-47857929-T-C

Position:

• chr14-47857929-T-C

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 0.768 in 151,948 control chromosomes in the GnomAD database, including 45,589 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 0.77 (45589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116690 AN: 151830 Hom.: 45570 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.768 AC: 116764 AN: 151948 Hom.: 45589 Cov.: 32 AF XY: 0.764 AC XY: 56746 AN XY: 74246

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.764

Alfa AF: 0.805 Hom.: 5861

Bravo AF: 0.757

Asia WGS AF: 0.687 AC: 2388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs373389; hg19: chr14-48327132;