rs1800875

Variant names:

• chr14-24510132-C-T
• rs1800875

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 0.41 in 151,962 control chromosomes in the GnomAD database, including 14,085 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 0.41 (14085 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62346 AN: 151844 Hom.: 14087 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.410 AC: 62362 AN: 151962 Hom.: 14085 Cov.: 31 AF XY: 0.405 AC XY: 30089 AN XY: 74244

African (AFR) AF: 0.256 AC: 10605 AN: 41458

American (AMR) AF: 0.298 AC: 4546 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1784 AN: 3470

East Asian (EAS) AF: 0.240 AC: 1240 AN: 5164

South Asian (SAS) AF: 0.419 AC: 2010 AN: 4800

European-Finnish (FIN) AF: 0.479 AC: 5054 AN: 10546

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35719 AN: 67952

Other (OTH) AF: 0.400 AC: 846 AN: 2114

Alfa AF: 0.457 Hom.: 8386

Bravo AF: 0.387

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.61
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1800875; hg19: chr14-24979338;