12-103520461-A-G

Variant names:

• chr12-103520461-A-G
• rs10861033
• XM_047428802.1:c.36+3651T>C

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.205-1240T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,024 control chromosomes in the GnomAD database, including 7,161 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 0.28 (7161 hom., cov: 32)
• Consequence: ENSG00000286197 ENST00000650784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 0 publications found

Genes affected

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

ENSG00000286197 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650784.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286197	ENST00000650784.1		n.205-1240T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42175 AN: 151908 Hom.: 7137 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.278 AC: 42246 AN: 152024 Hom.: 7161 Cov.: 32 AF XY: 0.280 AC XY: 20825 AN XY: 74316

African (AFR) AF: 0.448 AC: 18568 AN: 41430

American (AMR) AF: 0.231 AC: 3530 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3472

East Asian (EAS) AF: 0.515 AC: 2657 AN: 5160

South Asian (SAS) AF: 0.468 AC: 2250 AN: 4810

European-Finnish (FIN) AF: 0.140 AC: 1482 AN: 10582

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12129 AN: 67984

Other (OTH) AF: 0.265 AC: 557 AN: 2104

Alfa AF: 0.221 Hom.: 587

Bravo AF: 0.289

Asia WGS AF: 0.519 AC: 1802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10861033;

hg19: chr12-103914239;

COSMIC: COSV50457710;