12-103129777-C-T

Position:

• chr12-103129777-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386867.1(C12orf42):​c.*22-48240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 151,984 control chromosomes in the GnomAD database, including 8,118 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 0.32 (8118 hom., cov: 32)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

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

ENSG00000257703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.*22-48240G>A		intron_variant			NP_001373796.1
C12orf42	NR_170336.1	n.1120-48240G>A		intron_variant
C12orf42	XR_001748690.2	n.668+48352G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257703	ENST00000548415.2	n.339-48240G>A		intron_variant		4
ENSG00000257703	ENST00000548594.6	n.168-48240G>A		intron_variant		5
ENSG00000257703	ENST00000660834.1	n.192-48240G>A		intron_variant
ENSG00000257703	ENST00000667540.1	n.262-6337G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48266 AN: 151864 Hom.: 8107 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.318 AC: 48307 AN: 151984 Hom.: 8118 Cov.: 32 AF XY: 0.328 AC XY: 24376 AN XY: 74272

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.307

Alfa AF: 0.301 Hom.: 4129

Bravo AF: 0.310

Asia WGS AF: 0.391 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1818702; hg19: chr12-103523555;