rs871799

Variant names:

• chr1-203200743-C-G
• rs871799

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 0.181 in 152,100 control chromosomes in the GnomAD database, including 3,250 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 0.18 (3250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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: 0.181 AC: 27493 AN: 151982 Hom.: 3237 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.181 AC: 27542 AN: 152100 Hom.: 3250 Cov.: 32 AF XY: 0.183 AC XY: 13620 AN XY: 74350

African (AFR) AF: 0.287 AC: 11881 AN: 41452

American (AMR) AF: 0.221 AC: 3369 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 713 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2345 AN: 5156

South Asian (SAS) AF: 0.176 AC: 847 AN: 4818

European-Finnish (FIN) AF: 0.0481 AC: 510 AN: 10596

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7301 AN: 68016

Other (OTH) AF: 0.211 AC: 446 AN: 2110

Alfa AF: 0.140 Hom.: 248

Bravo AF: 0.204

Asia WGS AF: 0.307 AC: 1065 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs871799; hg19: chr1-203169871;