12-46092055-A-G

Variant names:

• chr12-46092055-A-G
• rs1373549

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 0.648 in 151,928 control chromosomes in the GnomAD database, including 32,359 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 0.65 (32359 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 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: 0.648 AC: 98307 AN: 151810 Hom.: 32315 Cov.: 30

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.648 AC: 98409 AN: 151928 Hom.: 32359 Cov.: 30 AF XY: 0.651 AC XY: 48336 AN XY: 74264

African (AFR) AF: 0.764 AC: 31613 AN: 41402

American (AMR) AF: 0.651 AC: 9935 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1926 AN: 3472

East Asian (EAS) AF: 0.730 AC: 3774 AN: 5172

South Asian (SAS) AF: 0.598 AC: 2875 AN: 4806

European-Finnish (FIN) AF: 0.674 AC: 7118 AN: 10564

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39261 AN: 67932

Other (OTH) AF: 0.599 AC: 1263 AN: 2110

Alfa AF: 0.598 Hom.: 127793

Bravo AF: 0.653

Asia WGS AF: 0.664 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.45
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1373549; hg19: chr12-46485838;