NM_198521.5:c.147+12071A>G

Variant names:

• chr12-103389536-T-C
• rs17568045
• NM_198521.5:c.147+12071A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_198521.5(C12orf42):​c.147+12071A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,326 control chromosomes in the GnomAD database, including 62 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 0.021 (62 hom., cov: 32)
• Consequence: C12orf42 NM_198521.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• 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=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0205 (3126/152326) while in subpopulation NFE AF = 0.03 (2042/68024). AF 95% confidence interval is 0.0289. There are 62 homozygotes in GnomAd4. There are 1586 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 62 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198521.5. 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_198521.5	MANE Select	c.147+12071A>G		intron	N/A	NP_940923.2
	C12orf42	NM_001099336.3		c.147+12071A>G		intron	N/A	NP_001092806.1
	C12orf42	NM_001386868.1		c.30+4846A>G		intron	N/A	NP_001373797.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf42	ENST00000548883.6	TSL:1 MANE Select	c.147+12071A>G		intron	N/A	ENSP00000447908.1
	C12orf42	ENST00000551134.5	TSL:1	n.147+12071A>G		intron	N/A	ENSP00000449447.1
	C12orf42	ENST00000378113.7	TSL:5	c.147+12071A>G		intron	N/A	ENSP00000367353.2

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3125 AN: 152208 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.00453

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0129

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00248

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0300

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0205 AC: 3126 AN: 152326 Hom.: 62 Cov.: 32 AF XY: 0.0213 AC XY: 1586 AN XY: 74498

African (AFR) AF: 0.00452 AC: 188 AN: 41580

American (AMR) AF: 0.0129 AC: 197 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4828

European-Finnish (FIN) AF: 0.0558 AC: 592 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0300 AC: 2042 AN: 68024

Other (OTH) AF: 0.0109 AC: 23 AN: 2112

Alfa AF: 0.0235 Hom.: 27

Bravo AF: 0.0173

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		-0.012
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17568045; hg19: chr12-103783314; COSMIC: COSV59390529;