1-202086810-A-G

Variant names:

• chr1-202086810-A-G
• rs10800812

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 0.772 in 152,192 control chromosomes in the GnomAD database, including 45,942 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 0.77 (45942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.885 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: 0.772 AC: 117448 AN: 152074 Hom.: 45899 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.772 AC: 117541 AN: 152192 Hom.: 45942 Cov.: 32 AF XY: 0.775 AC XY: 57662 AN XY: 74388

African (AFR) AF: 0.893 AC: 37100 AN: 41544

American (AMR) AF: 0.812 AC: 12418 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.667 AC: 3450 AN: 5172

South Asian (SAS) AF: 0.780 AC: 3760 AN: 4822

European-Finnish (FIN) AF: 0.714 AC: 7546 AN: 10576

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48201 AN: 68000

Other (OTH) AF: 0.759 AC: 1602 AN: 2112

Alfa AF: 0.732 Hom.: 80353

Bravo AF: 0.783

Asia WGS AF: 0.721 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.24
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10800812; hg19: chr1-202055938;