12-103129777-C-T

Variant names:

• chr12-103129777-C-T
• rs1818702
• NM_001386867.1:c.*22-48240G>A

Variant summary

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

The NM_001386867.1(C12orf42):​c.*22-48240G>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
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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.*22-48240G>A		intron	N/A	NP_001373796.1
	C12orf42	NR_170336.1		n.1120-48240G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257703	ENST00000548415.2	TSL:4	n.339-48240G>A		intron	N/A
	ENSG00000257703	ENST00000548594.6	TSL:5	n.168-48240G>A		intron	N/A
	ENSG00000257703	ENST00000660834.1		n.192-48240G>A		intron	N/A

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

African (AFR) AF: 0.284 AC: 11777 AN: 41448

American (AMR) AF: 0.361 AC: 5519 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.481 AC: 2477 AN: 5150

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5214 AN: 10534

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19859 AN: 67978

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.301 Hom.: 4510

Bravo AF: 0.310

Asia WGS AF: 0.391 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.43
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs1818702; hg19: chr12-103523555;