rs12037222

Variant names:

• chr1-39599289-G-A
• rs12037222

Your query was ambiguous. Multiple possible variants found:

• chr1-39599289-G-A
• chr1-39599289-G-C

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 0.162 in 152,132 control chromosomes in the GnomAD database, including 2,583 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 (2583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 47 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 = 0.23 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24663 AN: 152012 Hom.: 2586 Cov.: 32

Gnomad AFR AF: 0.0408

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.162 AC: 24657 AN: 152132 Hom.: 2583 Cov.: 32 AF XY: 0.160 AC XY: 11874 AN XY: 74376

African (AFR) AF: 0.0407 AC: 1689 AN: 41546

American (AMR) AF: 0.150 AC: 2291 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3470

East Asian (EAS) AF: 0.114 AC: 592 AN: 5186

South Asian (SAS) AF: 0.0746 AC: 360 AN: 4826

European-Finnish (FIN) AF: 0.229 AC: 2418 AN: 10560

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15860 AN: 67978

Other (OTH) AF: 0.179 AC: 377 AN: 2108

Alfa AF: 0.201 Hom.: 5802

Bravo AF: 0.153

Asia WGS AF: 0.0810 AC: 280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.52
DANN	Benign	0.30
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs12037222; hg19: chr1-40064961;