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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.162 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

Gnomad4 AFR AF: 0.0407

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.179

Alfa AF: 0.212 Hom.: 1321

Bravo AF: 0.153

Asia WGS AF: 0.0810 AC: 280 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	0.52
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12037222; hg19: chr1-40064961;