chr1-209814702-A-C

Variant names:

• chr1-209814702-A-C
• rs10863790

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 0.0451 in 152,244 control chromosomes in the GnomAD database, including 819 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 0.045 (819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.0451 AC: 6861 AN: 152126 Hom.: 814 Cov.: 32

Gnomad AFR AF: 0.00734

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0451 AC: 6872 AN: 152244 Hom.: 819 Cov.: 32 AF XY: 0.0517 AC XY: 3852 AN XY: 74444

African (AFR) AF: 0.00732 AC: 304 AN: 41546

American (AMR) AF: 0.182 AC: 2777 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2125 AN: 5164

South Asian (SAS) AF: 0.0955 AC: 460 AN: 4818

European-Finnish (FIN) AF: 0.0125 AC: 133 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 910 AN: 68020

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.0340 Hom.: 1885

Bravo AF: 0.0576

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.69
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10863790; hg19: chr1-209988047;