rs10861032

Positions:

• chr12-103518728-T-C
• chr12-103518728-T-G

Variant summary

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

The XM_047428802.1(C12orf42):​c.36+5384A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,080 control chromosomes in the GnomAD database, including 5,607 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 0.24 (5607 hom., cov: 32)
• Consequence: C12orf42 XM_047428802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

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

ENSG00000286197 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf42	XM_047428802.1	c.36+5384A>G		intron_variant			XP_047284758.1
C12orf42	XM_047428803.1	c.-21-40281A>G		intron_variant			XP_047284759.1
C12orf42	XM_011538294.3	c.36+5384A>G		intron_variant			XP_011536596.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286197	ENST00000650784.1	n.698A>G		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36502 AN: 151962 Hom.: 5587 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.240 AC: 36568 AN: 152080 Hom.: 5607 Cov.: 32 AF XY: 0.244 AC XY: 18177 AN XY: 74344

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.236

Alfa AF: 0.178 Hom.: 3397

Bravo AF: 0.250

Asia WGS AF: 0.501 AC: 1742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861032; hg19: chr12-103912506;