rs1800876

Variant names:

• chr14-24510007-G-A
• rs1800876

Your query was ambiguous. Multiple possible variants found:

• chr14-24510007-G-A
• chr14-24510007-G-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 0.243 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.243 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

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.270

Alfa AF: 0.252 Hom.: 2431

Bravo AF: 0.249

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800876; hg19: chr14-24979213;