rs1800807

Variant names:

• chr1-169632197-C-G
• rs1800807

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 0.58 in 151,828 control chromosomes in the GnomAD database, including 26,329 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 0.58 (26329 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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: 0.580 AC: 87971 AN: 151712 Hom.: 26297 Cov.: 30

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.580 AC: 88053 AN: 151828 Hom.: 26329 Cov.: 30 AF XY: 0.573 AC XY: 42529 AN XY: 74198

African (AFR) AF: 0.702 AC: 29037 AN: 41388

American (AMR) AF: 0.485 AC: 7409 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1486 AN: 5140

South Asian (SAS) AF: 0.483 AC: 2322 AN: 4810

European-Finnish (FIN) AF: 0.530 AC: 5572 AN: 10522

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38282 AN: 67914

Other (OTH) AF: 0.578 AC: 1219 AN: 2108

Alfa AF: 0.562 Hom.: 3054

Bravo AF: 0.581

Asia WGS AF: 0.391 AC: 1361 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1800807; hg19: chr1-169601435;