rs12036340

Variant names:

• chr1-162045950-A-G
• rs12036340

Your query was ambiguous. Multiple possible variants found:

• chr1-162045950-A-G
• chr1-162045950-A-T

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 0.246 in 151,902 control chromosomes in the GnomAD database, including 4,935 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 0.25 (4935 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.246 AC: 37326 AN: 151784 Hom.: 4934 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.246 AC: 37329 AN: 151902 Hom.: 4935 Cov.: 31 AF XY: 0.249 AC XY: 18461 AN XY: 74248

African (AFR) AF: 0.187 AC: 7730 AN: 41376

American (AMR) AF: 0.234 AC: 3567 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5158

South Asian (SAS) AF: 0.456 AC: 2196 AN: 4812

European-Finnish (FIN) AF: 0.247 AC: 2602 AN: 10554

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17379 AN: 67958

Other (OTH) AF: 0.252 AC: 531 AN: 2108

Alfa AF: 0.250 Hom.: 6401

Bravo AF: 0.237

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs12036340; hg19: chr1-162015740;