14-24662254-C-T

Variant names:

• chr14-24662254-C-T
• rs724023

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 0.717 in 151,994 control chromosomes in the GnomAD database, including 42,060 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 0.72 (42060 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.717 AC: 108967 AN: 151876 Hom.: 42049 Cov.: 30

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.717 AC: 109031 AN: 151994 Hom.: 42060 Cov.: 30 AF XY: 0.727 AC XY: 53983 AN XY: 74302

African (AFR) AF: 0.401 AC: 16576 AN: 41388

American (AMR) AF: 0.830 AC: 12674 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2958 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4610 AN: 5172

South Asian (SAS) AF: 0.814 AC: 3919 AN: 4816

European-Finnish (FIN) AF: 0.913 AC: 9658 AN: 10584

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56095 AN: 67992

Other (OTH) AF: 0.731 AC: 1540 AN: 2106

Alfa AF: 0.785 Hom.: 144701

Bravo AF: 0.697

Asia WGS AF: 0.812 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.7
DANN	Benign	0.40
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs724023; hg19: chr14-25131460;