rs1800875

Variant names:

• chr14-24510132-C-T
• rs1800875

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 0.41 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.411 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

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.400

Alfa AF: 0.463 Hom.: 3236

Bravo AF: 0.387

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800875; hg19: chr14-24979338;