rs1687827

Variant names:

• chr1-80229718-G-A
• rs1687827

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.680

Alfa AF: 0.731 Hom.: 5108

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1687827; hg19: chr1-80695403;