12-64324649-A-G

Variant names:

• chr12-64324649-A-G
• rs9332442
• NM_001170633.2:c.489-5669T>C

Variant summary

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

The NM_001170633.2(C12orf56):​c.489-5669T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,098 control chromosomes in the GnomAD database, including 15,585 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 0.45 (15585 hom., cov: 32)
• Consequence: C12orf56 NM_001170633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 3 publications found

Genes affected

C12orf56 (HGNC:26967): (chromosome 12 open reading frame 56)

ENSG00000293269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf56	NM_001170633.2	c.489-5669T>C		intron_variant	Intron 3 of 12	ENST00000543942.7	NP_001164104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf56	ENST00000543942.7	c.489-5669T>C		intron_variant	Intron 3 of 12	5	NM_001170633.2	ENSP00000446101.2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67968 AN: 151980 Hom.: 15569 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.447 AC: 68023 AN: 152098 Hom.: 15585 Cov.: 32 AF XY: 0.451 AC XY: 33548 AN XY: 74354

African (AFR) AF: 0.539 AC: 22336 AN: 41472

American (AMR) AF: 0.416 AC: 6350 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1619 AN: 3472

East Asian (EAS) AF: 0.331 AC: 1717 AN: 5180

South Asian (SAS) AF: 0.407 AC: 1961 AN: 4820

European-Finnish (FIN) AF: 0.527 AC: 5580 AN: 10584

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27352 AN: 67978

Other (OTH) AF: 0.408 AC: 863 AN: 2114

Alfa AF: 0.427 Hom.: 2370

Bravo AF: 0.438

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.51
PhyloP100		0.81
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9332442; hg19: chr12-64718429;