12-103163194-T-A

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001386867.1(C12orf42):​c.*21+14935A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).

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>T		intron	N/A	NP_001373796.1
	C12orf42-AS1	NR_126333.1		n.547+244T>A		intron	N/A
	C12orf42	NR_170336.1		n.1119+14935A>T		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>A		intron	N/A
	ENSG00000257703	ENST00000548415.2	TSL:4	n.338+14935A>T		intron	N/A
	ENSG00000257703	ENST00000548594.6	TSL:5	n.167+14935A>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
DANN	Benign	0.67
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;