rs1018730

Variant names:

• chr1-155941039-G-A
• rs1018730

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 0.812 in 152,178 control chromosomes in the GnomAD database, including 52,306 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 0.81 (52306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 8 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 = 0.918 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123513 AN: 152060 Hom.: 52293 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.812 AC: 123546 AN: 152178 Hom.: 52306 Cov.: 32 AF XY: 0.813 AC XY: 60494 AN XY: 74384

African (AFR) AF: 0.543 AC: 22518 AN: 41452

American (AMR) AF: 0.908 AC: 13887 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.939 AC: 4868 AN: 5182

South Asian (SAS) AF: 0.866 AC: 4183 AN: 4832

European-Finnish (FIN) AF: 0.892 AC: 9461 AN: 10610

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62855 AN: 68016

Other (OTH) AF: 0.844 AC: 1786 AN: 2116

Alfa AF: 0.888 Hom.: 77544

Bravo AF: 0.802

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.26
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1018730; hg19: chr1-155910830;