rs12046272

chr1-105532022-A-G

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 0.0277 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.00823

Gnomad4 AMR AF: 0.0874

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.0766

Gnomad4 FIN AF: 0.00560

Gnomad4 NFE AF: 0.00954

Gnomad4 OTH AF: 0.0298

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.63
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12046272; hg19: chr1-106074644;