chr1-186230352-G-A

Variant names:

• chr1-186230352-G-A
• rs586281

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 0.158 in 152,128 control chromosomes in the GnomAD database, including 2,474 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 0.16 (2474 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 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: 0.158 AC: 24093 AN: 152010 Hom.: 2475 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.158 AC: 24094 AN: 152128 Hom.: 2474 Cov.: 32 AF XY: 0.161 AC XY: 11934 AN XY: 74344

African (AFR) AF: 0.0468 AC: 1943 AN: 41526

American (AMR) AF: 0.105 AC: 1606 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3466

East Asian (EAS) AF: 0.122 AC: 634 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1012 AN: 4812

European-Finnish (FIN) AF: 0.282 AC: 2983 AN: 10566

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15011 AN: 67982

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.186 Hom.: 404

Bravo AF: 0.137

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs586281; hg19: chr1-186199484;