12-103256253-T-C

Variant names:

• chr12-103256253-T-C
• rs4433630
• NM_001386867.1:c.320+20897A>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.320+20897A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 147,420 control chromosomes in the GnomAD database, including 23,306 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 0.56 (23306 hom., cov: 23)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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.320+20897A>G		intron	N/A	NP_001373796.1
	C12orf42	NR_103526.2		n.1778+7073A>G		intron	N/A
	C12orf42	NR_170332.1		n.1582+7073A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42	ENST00000547347.5	TSL:2	n.*1366+7073A>G		intron	N/A	ENSP00000446908.1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 82484 AN: 147338 Hom.: 23295 Cov.: 23

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.560 AC: 82520 AN: 147420 Hom.: 23306 Cov.: 23 AF XY: 0.562 AC XY: 40320 AN XY: 71768

African (AFR) AF: 0.637 AC: 25381 AN: 39854

American (AMR) AF: 0.527 AC: 7733 AN: 14662

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1742 AN: 3454

East Asian (EAS) AF: 0.696 AC: 3516 AN: 5054

South Asian (SAS) AF: 0.664 AC: 3058 AN: 4604

European-Finnish (FIN) AF: 0.482 AC: 4528 AN: 9394

Middle Eastern (MID) AF: 0.616 AC: 170 AN: 276

European-Non Finnish (NFE) AF: 0.518 AC: 34798 AN: 67204

Other (OTH) AF: 0.566 AC: 1152 AN: 2034

Alfa AF: 0.532 Hom.: 36059

Bravo AF: 0.560

Asia WGS AF: 0.695 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.69
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4433630; hg19: chr12-103650031;