chr14-23833464-C-T

Position:

• chr14-23833464-C-T

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 0.2 in 152,090 control chromosomes in the GnomAD database, including 3,325 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 0.20 (3325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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: 0.200 AC: 30416 AN: 151972 Hom.: 3325 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.200 AC: 30426 AN: 152090 Hom.: 3325 Cov.: 32 AF XY: 0.203 AC XY: 15060 AN XY: 74362

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.195

Alfa AF: 0.215 Hom.: 7612

Bravo AF: 0.188

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12050360; hg19: chr14-24302673;