12-103101373-T-C

Position:

• chr12-103101373-T-C

Variant summary

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

The NM_001386867.1(C12orf42):​c.*22-19836A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 152,060 control chromosomes in the GnomAD database, including 26,224 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 0.57 (26224 hom., cov: 32)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.*22-19836A>G		intron_variant			NP_001373796.1
C12orf42	NR_170336.1	n.1120-19836A>G		intron_variant
C12orf42	XR_001748690.2	n.669-53047A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257703	ENST00000548415.2	n.339-19836A>G		intron_variant		4
ENSG00000257703	ENST00000548594.6	n.168-19836A>G		intron_variant		5
ENSG00000257703	ENST00000660834.1	n.192-19836A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87284 AN: 151942 Hom.: 26185 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.575 AC: 87386 AN: 152060 Hom.: 26224 Cov.: 32 AF XY: 0.580 AC XY: 43089 AN XY: 74332

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.530

Alfa AF: 0.485 Hom.: 39924

Bravo AF: 0.583

Asia WGS AF: 0.679 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10778213; hg19: chr12-103495151;