rs1800808

Positions:

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

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 0.0982 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

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 (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.111

Alfa AF: 0.103 Hom.: 142

Bravo AF: 0.0934

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800808; hg19: chr1-169601129;