12-103269117-T-C

Position:

• chr12-103269117-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+8033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,026 control chromosomes in the GnomAD database, including 5,135 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 0.25 (5135 hom., cov: 32)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.320+8033A>G		intron_variant			NP_001373796.1
C12orf42	XM_011538312.3	c.420+690A>G		intron_variant			XP_011536614.1
C12orf42	XM_011538315.3	c.465-155A>G		intron_variant			XP_011536617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf42	ENST00000547347.5	c.*136-155A>G		intron_variant, NMD_transcript_variant		2		ENSP00000446908
C12orf42	ENST00000546526.5	n.446-155A>G		intron_variant, non_coding_transcript_variant		3
C12orf42	ENST00000549927.5	n.48-155A>G		intron_variant, non_coding_transcript_variant		5
C12orf42	ENST00000550650.5	n.413+690A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38348 AN: 151906 Hom.: 5136 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.252 AC: 38341 AN: 152026 Hom.: 5135 Cov.: 32 AF XY: 0.258 AC XY: 19204 AN XY: 74306

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.252

Alfa AF: 0.136 Hom.: 235

Bravo AF: 0.242

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520191; hg19: chr12-103662895;