12-51928262-T-C

Variant names:

• chr12-51928262-T-C
• rs12230575

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 0.0848 in 152,248 control chromosomes in the GnomAD database, including 597 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 0.085 (597 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0856 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: 0.0849 AC: 12920 AN: 152128 Hom.: 597 Cov.: 33

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0875

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0848 AC: 12917 AN: 152248 Hom.: 597 Cov.: 33 AF XY: 0.0853 AC XY: 6351 AN XY: 74454

African (AFR) AF: 0.0723 AC: 3005 AN: 41544

American (AMR) AF: 0.0848 AC: 1297 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3472

East Asian (EAS) AF: 0.0903 AC: 467 AN: 5172

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1348 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0875 AC: 5951 AN: 68016

Other (OTH) AF: 0.0851 AC: 180 AN: 2114

Alfa AF: 0.0848 Hom.: 312

Bravo AF: 0.0824

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.1
DANN	Benign	0.85
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12230575; hg19: chr12-52322046;