rs10800309

Variant names:

• chr1-161502368-A-G
• rs10800309

Your query was ambiguous. Multiple possible variants found:

• chr1-161502368-A-G
• chr1-161502368-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 0.658 in 152,156 control chromosomes in the GnomAD database, including 33,717 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 0.66 (33717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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: 0.658 AC: 100031 AN: 152038 Hom.: 33689 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.658 AC: 100115 AN: 152156 Hom.: 33717 Cov.: 32 AF XY: 0.652 AC XY: 48500 AN XY: 74378

African (AFR) AF: 0.736 AC: 30554 AN: 41502

American (AMR) AF: 0.598 AC: 9152 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3470

East Asian (EAS) AF: 0.272 AC: 1407 AN: 5170

South Asian (SAS) AF: 0.523 AC: 2520 AN: 4822

European-Finnish (FIN) AF: 0.644 AC: 6819 AN: 10594

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45167 AN: 67982

Other (OTH) AF: 0.645 AC: 1363 AN: 2114

Alfa AF: 0.655 Hom.: 142947

Bravo AF: 0.664

Asia WGS AF: 0.437 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.38
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10800309; hg19: chr1-161472158;