12-103256253-T-C

Position:

• chr12-103256253-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.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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C12orf42	NM_001386867.1	c.320+20897A>G		intron_variant
C12orf42	XM_017019281.2	c.500+7073A>G		intron_variant
C12orf42	XM_047428807.1	c.443+7073A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf42	ENST00000547347.5	c.*1366+7073A>G		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.566

Alfa AF: 0.531 Hom.: 28404

Bravo AF: 0.560

Asia WGS AF: 0.695 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4433630; hg19: chr12-103650031;