12-49282227-T-C

Variant names:

• chr12-49282227-T-C
• rs10875943

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 0.417 in 151,856 control chromosomes in the GnomAD database, including 15,500 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 0.42 (15500 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.870
• Publications: 71 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 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: 0.416 AC: 63168 AN: 151738 Hom.: 15450 Cov.: 30

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.417 AC: 63281 AN: 151856 Hom.: 15500 Cov.: 30 AF XY: 0.423 AC XY: 31392 AN XY: 74200

African (AFR) AF: 0.627 AC: 25970 AN: 41398

American (AMR) AF: 0.313 AC: 4771 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1018 AN: 3466

East Asian (EAS) AF: 0.837 AC: 4327 AN: 5168

South Asian (SAS) AF: 0.606 AC: 2918 AN: 4812

European-Finnish (FIN) AF: 0.353 AC: 3712 AN: 10528

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

European-Non Finnish (NFE) AF: 0.284 AC: 19318 AN: 67910

Other (OTH) AF: 0.387 AC: 815 AN: 2106

Alfa AF: 0.321 Hom.: 36235

Bravo AF: 0.417

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	10
DANN	Benign	0.71
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs10875943; hg19: chr12-49676010;