rs17568045

Positions:

• chr12-103389536-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000548883.6(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 ENST00000548883.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

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=-0.91).
• 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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 62 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	NM_198521.5	c.147+12071A>G		intron_variant		ENST00000548883.6	NP_940923.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf42	ENST00000548883.6	c.147+12071A>G		intron_variant		1	NM_198521.5	ENSP00000447908	P2

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

Gnomad4 AFR AF: 0.00452

Gnomad4 AMR AF: 0.0129

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.0558

Gnomad4 NFE AF: 0.0300

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0230 Hom.: 22

Bravo AF: 0.0173

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.70

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

Publications

LitVar

Other links and lift over

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