rs1800805

Variant names:

• chr1-169632043-C-T
• rs1800805

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 0.309 in 151,988 control chromosomes in the GnomAD database, including 8,165 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 0.31 (8165 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 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: 0.309 AC: 46924 AN: 151870 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.309 AC: 46923 AN: 151988 Hom.: 8165 Cov.: 32 AF XY: 0.303 AC XY: 22481 AN XY: 74294

African (AFR) AF: 0.170 AC: 7069 AN: 41464

American (AMR) AF: 0.255 AC: 3895 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5168

South Asian (SAS) AF: 0.252 AC: 1210 AN: 4806

European-Finnish (FIN) AF: 0.328 AC: 3458 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27492 AN: 67946

Other (OTH) AF: 0.336 AC: 709 AN: 2112

Alfa AF: 0.374 Hom.: 42476

Bravo AF: 0.299

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1800805; hg19: chr1-169601281;