chr12-103089316-A-G

Variant names:

• chr12-103089316-A-G
• rs10745954
• NM_001386867.1:c.*22-7779T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386867.1(C12orf42):​c.*22-7779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 151,830 control chromosomes in the GnomAD database, including 29,078 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 0.60 (29078 hom., cov: 30)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

Genes affected

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

ENSG00000257703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.*22-7779T>C		intron_variant	Intron 6 of 6		NP_001373796.1
C12orf42	NR_170336.1	n.1120-7779T>C		intron_variant	Intron 10 of 10
C12orf42	XR_001748690.2	n.669-40990T>C		intron_variant	Intron 10 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257703	ENST00000548415.2	n.339-7779T>C		intron_variant	Intron 2 of 2	4
ENSG00000257703	ENST00000548594.6	n.168-7779T>C		intron_variant	Intron 2 of 2	5
ENSG00000257703	ENST00000660834.1	n.192-7779T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91460 AN: 151712 Hom.: 29027 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.603 AC: 91574 AN: 151830 Hom.: 29078 Cov.: 30 AF XY: 0.609 AC XY: 45214 AN XY: 74188

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.558

Alfa AF: 0.501 Hom.: 22607

Bravo AF: 0.613

Asia WGS AF: 0.692 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10745954; hg19: chr12-103483094;