rs10878151

Variant names:

• chr12-64336618-G-A
• rs10878151
• NM_001170633.2:c.416-5586C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-64336618-G-A
• chr12-64336618-G-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.416-5586C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,850 control chromosomes in the GnomAD database, including 30,130 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 0.63 (30130 hom., cov: 30)
• Consequence: C12orf56 NM_001170633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001170633.2. 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
	C12orf56	NM_001170633.2	MANE Select	c.416-5586C>T		intron	N/A	NP_001164104.1	Q8IXR9-1
	C12orf56	NM_001099676.3		c.416-5586C>T		intron	N/A	NP_001093146.1	Q8IXR9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf56	ENST00000543942.7	TSL:5 MANE Select	c.416-5586C>T		intron	N/A	ENSP00000446101.2	Q8IXR9-1
	C12orf56	ENST00000333722.9	TSL:1	c.416-5586C>T		intron	N/A	ENSP00000329698.5	Q8IXR9-2
	C12orf56	ENST00000924490.1		c.416-5586C>T		intron	N/A	ENSP00000594549.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95064 AN: 151732 Hom.: 30125 Cov.: 30

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.626 AC: 95097 AN: 151850 Hom.: 30130 Cov.: 30 AF XY: 0.627 AC XY: 46551 AN XY: 74200

African (AFR) AF: 0.515 AC: 21306 AN: 41358

American (AMR) AF: 0.668 AC: 10197 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2264 AN: 3470

East Asian (EAS) AF: 0.662 AC: 3413 AN: 5154

South Asian (SAS) AF: 0.637 AC: 3064 AN: 4808

European-Finnish (FIN) AF: 0.680 AC: 7169 AN: 10542

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45319 AN: 67936

Other (OTH) AF: 0.644 AC: 1362 AN: 2114

Alfa AF: 0.664 Hom.: 53429

Bravo AF: 0.626

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		0.87
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: rs10878151; hg19: chr12-64730398;