12-103547286-G-A

Variant names:

• chr12-103547286-G-A
• rs12578202
• ENST00000650784.1:n.204+16361C>T

Variant summary

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

The ENST00000650784.1(ENSG00000286197):​n.204+16361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,104 control chromosomes in the GnomAD database, including 1,663 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 0.13 (1663 hom., cov: 32)
• Consequence: ENSG00000286197 ENST00000650784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

Genes affected

ENSG00000286197 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286197	ENST00000650784.1		n.204+16361C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20466 AN: 151986 Hom.: 1657 Cov.: 32

Gnomad AFR AF: 0.0563

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.135 AC: 20483 AN: 152104 Hom.: 1663 Cov.: 32 AF XY: 0.138 AC XY: 10267 AN XY: 74350

African (AFR) AF: 0.0563 AC: 2338 AN: 41500

American (AMR) AF: 0.127 AC: 1940 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5170

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1577 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10799 AN: 67980

Other (OTH) AF: 0.157 AC: 331 AN: 2104

Alfa AF: 0.153 Hom.: 2311

Bravo AF: 0.129

Asia WGS AF: 0.252 AC: 877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs12578202; hg19: chr12-103941064;