rs1687827

Variant names:

• chr1-80229718-G-A
• rs1687827

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 0.697 in 152,016 control chromosomes in the GnomAD database, including 37,713 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 0.70 (37713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.697 AC: 105893 AN: 151898 Hom.: 37693 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.697 AC: 105957 AN: 152016 Hom.: 37713 Cov.: 32 AF XY: 0.700 AC XY: 52030 AN XY: 74284

African (AFR) AF: 0.545 AC: 22564 AN: 41420

American (AMR) AF: 0.743 AC: 11347 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2424 AN: 3472

East Asian (EAS) AF: 0.856 AC: 4425 AN: 5172

South Asian (SAS) AF: 0.771 AC: 3718 AN: 4822

European-Finnish (FIN) AF: 0.738 AC: 7801 AN: 10574

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51266 AN: 67972

Other (OTH) AF: 0.680 AC: 1437 AN: 2112

Alfa AF: 0.723 Hom.: 5219

Bravo AF: 0.692

Asia WGS AF: 0.826 AC: 2862 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1687827; hg19: chr1-80695403;