1-162066689-G-A

Variant names:

• chr1-162066689-G-A
• rs12567209

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 0.0888 in 152,094 control chromosomes in the GnomAD database, including 737 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 0.089 (737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 22 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 (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0888 AC: 13503 AN: 151976 Hom.: 738 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0888 AC: 13509 AN: 152094 Hom.: 737 Cov.: 32 AF XY: 0.0926 AC XY: 6882 AN XY: 74344

African (AFR) AF: 0.0739 AC: 3066 AN: 41484

American (AMR) AF: 0.119 AC: 1823 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0770 AC: 267 AN: 3468

East Asian (EAS) AF: 0.166 AC: 859 AN: 5174

South Asian (SAS) AF: 0.216 AC: 1040 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1128 AN: 10556

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0740 AC: 5035 AN: 68006

Other (OTH) AF: 0.0917 AC: 193 AN: 2104

Alfa AF: 0.0751 Hom.: 772

Bravo AF: 0.0857

Asia WGS AF: 0.186 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.60
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12567209; hg19: chr1-162036479;