rs1800794

Variant names:

• chr2-112785696-G-A
• rs1800794
• ENST00000762706.1:n.404+14800G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762706.1(ENSG00000299339):​n.404+14800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 13 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.404+14800G>A		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+14800G>A		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+14800G>A		intron	N/A

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

African (AFR) AF: 0.0543 AC: 2253 AN: 41514

American (AMR) AF: 0.244 AC: 3740 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1130 AN: 3472

East Asian (EAS) AF: 0.0792 AC: 411 AN: 5188

South Asian (SAS) AF: 0.289 AC: 1397 AN: 4828

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19932 AN: 67978

Other (OTH) AF: 0.230 AC: 485 AN: 2106

Alfa AF: 0.246 Hom.: 868

Bravo AF: 0.202

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.4
DANN	Benign	0.75
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1800794; hg19: chr2-113543273;