rs12046272

Variant names:

• chr1-105532022-A-G
• rs12046272

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 0.0277 in 152,074 control chromosomes in the GnomAD database, including 294 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 0.028 (294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0277 AC: 4210 AN: 151956 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.00825

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.00560

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00953

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0277 AC: 4212 AN: 152074 Hom.: 294 Cov.: 32 AF XY: 0.0315 AC XY: 2341 AN XY: 74358

African (AFR) AF: 0.00823 AC: 342 AN: 41552

American (AMR) AF: 0.0874 AC: 1333 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3468

East Asian (EAS) AF: 0.261 AC: 1344 AN: 5148

South Asian (SAS) AF: 0.0766 AC: 370 AN: 4830

European-Finnish (FIN) AF: 0.00560 AC: 59 AN: 10542

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00954 AC: 648 AN: 67958

Other (OTH) AF: 0.0298 AC: 63 AN: 2112

Alfa AF: 0.0157 Hom.: 12

Bravo AF: 0.0351

Asia WGS AF: 0.130 AC: 451 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12046272; hg19: chr1-106074644;