14-24802314-T-C

Variant names:

• chr14-24802314-T-C
• rs854384

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.810 AC: 33595 AN: 41488

American (AMR) AF: 0.858 AC: 13130 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2971 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5161 AN: 5184

South Asian (SAS) AF: 0.815 AC: 3932 AN: 4826

European-Finnish (FIN) AF: 0.836 AC: 8856 AN: 10594

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55034 AN: 68022

Other (OTH) AF: 0.831 AC: 1758 AN: 2116

Alfa AF: 0.815 Hom.: 181004

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs854384; hg19: chr14-25271520;