rs1800794

Variant names:

• chr2-112785696-G-A
• rs1800794

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 0.218 in 152,162 control chromosomes in the GnomAD database, including 4,587 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 0.22 (4587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.218 AC: 33153 AN: 152044 Hom.: 4589 Cov.: 33

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.218 AC: 33152 AN: 152162 Hom.: 4587 Cov.: 33 AF XY: 0.220 AC XY: 16373 AN XY: 74382

Gnomad4 AFR AF: 0.0543

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0792

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.230

Alfa AF: 0.250 Hom.: 858

Bravo AF: 0.202

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800794; hg19: chr2-113543273;