12-103163194-T-C

Variant names:

• chr12-103163194-T-C
• rs2292996
• NM_001386867.1:c.*21+14935A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386867.1(C12orf42):​c.*21+14935A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,962 control chromosomes in the GnomAD database, including 30,655 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 0.61 (30655 hom., cov: 31)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96
• Publications: 3 publications found

Genes affected

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

C12orf42-AS1 (HGNC:56185): (C12orf42 antisense RNA 1)

ENSG00000257703 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386867.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42	NM_001386867.1		c.*21+14935A>G		intron	N/A	NP_001373796.1
	C12orf42-AS1	NR_126333.1		n.547+244T>C		intron	N/A
	C12orf42	NR_170336.1		n.1119+14935A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42-AS1	ENST00000547418.5	TSL:5	n.547+244T>C		intron	N/A
	ENSG00000257703	ENST00000548415.2	TSL:4	n.338+14935A>G		intron	N/A
	ENSG00000257703	ENST00000548594.6	TSL:5	n.167+14935A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93296 AN: 151844 Hom.: 30592 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.615 AC: 93424 AN: 151962 Hom.: 30655 Cov.: 31 AF XY: 0.623 AC XY: 46248 AN XY: 74260

African (AFR) AF: 0.826 AC: 34237 AN: 41458

American (AMR) AF: 0.572 AC: 8733 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3468

East Asian (EAS) AF: 0.848 AC: 4385 AN: 5170

South Asian (SAS) AF: 0.568 AC: 2734 AN: 4816

European-Finnish (FIN) AF: 0.672 AC: 7087 AN: 10546

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32783 AN: 67928

Other (OTH) AF: 0.564 AC: 1189 AN: 2110

Alfa AF: 0.550 Hom.: 21857

Bravo AF: 0.621

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.69
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs2292996; hg19: chr12-103556972;