14-24510007-G-A

Variant names:

• chr14-24510007-G-A
• rs1800876

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 0.243 in 151,956 control chromosomes in the GnomAD database, including 5,708 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 0.24 (5708 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36877 AN: 151838 Hom.: 5699 Cov.: 31

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.243 AC: 36897 AN: 151956 Hom.: 5708 Cov.: 31 AF XY: 0.254 AC XY: 18836 AN XY: 74242

African (AFR) AF: 0.0762 AC: 3162 AN: 41482

American (AMR) AF: 0.451 AC: 6881 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1133 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2122 AN: 5156

South Asian (SAS) AF: 0.262 AC: 1261 AN: 4804

European-Finnish (FIN) AF: 0.346 AC: 3640 AN: 10524

Middle Eastern (MID) AF: 0.330 AC: 95 AN: 288

European-Non Finnish (NFE) AF: 0.261 AC: 17717 AN: 67958

Other (OTH) AF: 0.270 AC: 570 AN: 2108

Alfa AF: 0.252 Hom.: 2733

Bravo AF: 0.249

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.74
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1800876; hg19: chr14-24979213;