12-93655848-C-T

Variant names:

• chr12-93655848-C-T
• rs10492322

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 0.0379 in 151,830 control chromosomes in the GnomAD database, including 297 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 0.038 (297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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: 0.0378 AC: 5736 AN: 151712 Hom.: 294 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.000943

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00325

Gnomad OTH AF: 0.0317

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

GnomAD4 genome AF: 0.0379 AC: 5757 AN: 151830 Hom.: 297 Cov.: 32 AF XY: 0.0374 AC XY: 2780 AN XY: 74266

African (AFR) AF: 0.114 AC: 4701 AN: 41156

American (AMR) AF: 0.0153 AC: 234 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00951 AC: 33 AN: 3470

East Asian (EAS) AF: 0.0551 AC: 285 AN: 5174

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4822

European-Finnish (FIN) AF: 0.000943 AC: 10 AN: 10604

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00325 AC: 221 AN: 68012

Other (OTH) AF: 0.0314 AC: 66 AN: 2102

Alfa AF: 0.0138 Hom.: 62

Bravo AF: 0.0433

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.54
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10492322; hg19: chr12-94049624;