rs10878151

Positions:

• chr12-64336618-G-A
• chr12-64336618-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf56	NM_001170633.2	c.416-5586C>T		intron_variant		ENST00000543942.7	NP_001164104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf56	ENST00000543942.7	c.416-5586C>T		intron_variant		5	NM_001170633.2	ENSP00000446101	P1
C12orf56	ENST00000333722.9	c.416-5586C>T		intron_variant		1		ENSP00000329698
	ENST00000535684.6	n.324-52415G>A		intron_variant, non_coding_transcript_variant		2
C12orf56	ENST00000543259.1	c.377-5586C>T		intron_variant		4		ENSP00000443341

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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.644

Alfa AF: 0.666 Hom.: 45775

Bravo AF: 0.626

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs10878151; hg19: chr12-64730398;