rs1687827

Positions:

• chr1-80229718-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.80229718G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;