12-103089316-A-G

Variant names:

• chr12-103089316-A-G
• rs10745954
• NM_001386867.1:c.*22-7779T>C

Variant summary

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

The NM_001386867.1(C12orf42):​c.*22-7779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,830 control chromosomes in the GnomAD database, including 29,078 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 0.60 (29078 hom., cov: 30)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 30 publications found

Genes affected

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

ENSG00000257703 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 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.*22-7779T>C		intron	N/A	NP_001373796.1
	C12orf42	NR_170336.1		n.1120-7779T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257703	ENST00000548415.2	TSL:4	n.339-7779T>C		intron	N/A
	ENSG00000257703	ENST00000548594.6	TSL:5	n.168-7779T>C		intron	N/A
	ENSG00000257703	ENST00000660834.1		n.192-7779T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91460 AN: 151712 Hom.: 29027 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.603 AC: 91574 AN: 151830 Hom.: 29078 Cov.: 30 AF XY: 0.609 AC XY: 45214 AN XY: 74188

African (AFR) AF: 0.792 AC: 32822 AN: 41416

American (AMR) AF: 0.606 AC: 9257 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1474 AN: 3470

East Asian (EAS) AF: 0.773 AC: 3972 AN: 5138

South Asian (SAS) AF: 0.559 AC: 2691 AN: 4816

European-Finnish (FIN) AF: 0.633 AC: 6654 AN: 10518

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32845 AN: 67900

Other (OTH) AF: 0.558 AC: 1172 AN: 2102

Alfa AF: 0.520 Hom.: 61529

Bravo AF: 0.613

Asia WGS AF: 0.692 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.51
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10745954; hg19: chr12-103483094;