chr14-24802314-T-C

Variant names:

• chr14-24802314-T-C
• rs854384

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 0.824 in 152,204 control chromosomes in the GnomAD database, including 51,800 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 0.82 (51800 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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 = 0.973 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: 0.824 AC: 125346 AN: 152086 Hom.: 51755 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.824 AC: 125451 AN: 152204 Hom.: 51800 Cov.: 33 AF XY: 0.828 AC XY: 61628 AN XY: 74416

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.831

Alfa AF: 0.815 Hom.: 116548

Bravo AF: 0.826

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs854384; hg19: chr14-25271520;