rs1800808

Variant names:

• chr1-169631891-A-G
• rs1800808

Your query was ambiguous. Multiple possible variants found:

• chr1-169631891-A-G
• chr1-169631891-A-T

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 0.0982 in 152,116 control chromosomes in the GnomAD database, including 929 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 0.098 (929 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14944 AN: 151998 Hom.: 932 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0982 AC: 14933 AN: 152116 Hom.: 929 Cov.: 31 AF XY: 0.0979 AC XY: 7282 AN XY: 74382

African (AFR) AF: 0.0323 AC: 1342 AN: 41506

American (AMR) AF: 0.0729 AC: 1114 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1056 AN: 5170

South Asian (SAS) AF: 0.120 AC: 578 AN: 4812

European-Finnish (FIN) AF: 0.125 AC: 1329 AN: 10596

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8506 AN: 67964

Other (OTH) AF: 0.111 AC: 235 AN: 2112

Alfa AF: 0.101 Hom.: 142

Bravo AF: 0.0934

Asia WGS AF: 0.148 AC: 514 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	5.4
DANN	Benign	0.48
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1800808; hg19: chr1-169601129;