12-103163194-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

ENSG00000257703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.*21+14935A>G		intron_variant	Intron 6 of 6		NP_001373796.1
C12orf42-AS1	NR_126333.1	n.547+244T>C		intron_variant	Intron 4 of 6
C12orf42	NR_170336.1	n.1119+14935A>G		intron_variant	Intron 10 of 10
C12orf42	XR_001748690.2	n.668+14935A>G		intron_variant	Intron 10 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf42-AS1	ENST00000547418.5	n.547+244T>C		intron_variant	Intron 4 of 6	5
ENSG00000257703	ENST00000548415.2	n.338+14935A>G		intron_variant	Intron 2 of 2	4
ENSG00000257703	ENST00000548594.6	n.167+14935A>G		intron_variant	Intron 2 of 2	5

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

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.564

Alfa AF: 0.522 Hom.: 14581

Bravo AF: 0.621

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2292996; hg19: chr12-103556972;