12-103101373-T-C

Variant names:

• chr12-103101373-T-C
• rs10778213
• NM_001386867.1:c.*22-19836A>G

Variant summary

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

The NM_001386867.1(C12orf42):​c.*22-19836A>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
• Publications: 20 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42	NM_001386867.1		c.*22-19836A>G		intron	N/A	NP_001373796.1
	C12orf42	NR_170336.1		n.1120-19836A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257703	ENST00000548415.2	TSL:4	n.339-19836A>G		intron	N/A
	ENSG00000257703	ENST00000548594.6	TSL:5	n.168-19836A>G		intron	N/A
	ENSG00000257703	ENST00000660834.1		n.192-19836A>G		intron	N/A

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

African (AFR) AF: 0.726 AC: 30105 AN: 41466

American (AMR) AF: 0.583 AC: 8901 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4241 AN: 5178

South Asian (SAS) AF: 0.539 AC: 2600 AN: 4824

European-Finnish (FIN) AF: 0.589 AC: 6223 AN: 10570

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32161 AN: 67966

Other (OTH) AF: 0.530 AC: 1118 AN: 2110

Alfa AF: 0.502 Hom.: 85748

Bravo AF: 0.583

Asia WGS AF: 0.679 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.51
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs10778213; hg19: chr12-103495151;