12-103269117-T-C

Variant names:

• chr12-103269117-T-C
• rs1520191
• XR_001748691.2:n.597A>G

Variant summary

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

The XR_001748691.2(C12orf42):​n.597A>G variant causes a non coding transcript exon 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 XR_001748691.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 1 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546526.5. 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+8033A>G		intron	N/A	NP_001373796.1
	C12orf42	NR_103526.2		n.548-155A>G		intron	N/A
	C12orf42	NR_170332.1		n.427-155A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42	ENST00000546526.5	TSL:3	n.446-155A>G		intron	N/A
	C12orf42	ENST00000547347.5	TSL:2	n.*136-155A>G		intron	N/A	ENSP00000446908.1
	C12orf42	ENST00000549927.5	TSL:5	n.48-155A>G		intron	N/A

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

African (AFR) AF: 0.190 AC: 7894 AN: 41490

American (AMR) AF: 0.250 AC: 3810 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3464

East Asian (EAS) AF: 0.526 AC: 2715 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1982 AN: 4808

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10576

Middle Eastern (MID) AF: 0.276 AC: 80 AN: 290

European-Non Finnish (NFE) AF: 0.248 AC: 16829 AN: 67948

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.138 Hom.: 252

Bravo AF: 0.242

Asia WGS AF: 0.453 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.67
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1520191; hg19: chr12-103662895;