1-117590608-G-C

Variant names:

• chr1-117590608-G-C
• rs12730116

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 0.146 in 152,218 control chromosomes in the GnomAD database, including 1,653 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 0.15 (1653 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.191 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: 0.146 AC: 22215 AN: 152100 Hom.: 1645 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0946

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.146 AC: 22243 AN: 152218 Hom.: 1653 Cov.: 33 AF XY: 0.151 AC XY: 11229 AN XY: 74418

African (AFR) AF: 0.139 AC: 5773 AN: 41526

American (AMR) AF: 0.197 AC: 3018 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.0941 AC: 488 AN: 5188

South Asian (SAS) AF: 0.194 AC: 937 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1772 AN: 10592

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9412 AN: 67992

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.0614 Hom.: 66

Bravo AF: 0.146

Asia WGS AF: 0.171 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.50
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs12730116; hg19: chr1-118133230;