rs7487873

chr12-64333676-A-Cchr12-64333676-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170633.2(C12orf56):c.416-2644T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,802 control chromosomes in the GnomAD database, including 22,651 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 0.54 (22651 hom., cov: 31)
• Consequence: C12orf56 NM_001170633.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C12orf56	NM_001170633.2	c.416-2644T>G		intron_variant		ENST00000543942.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf56	ENST00000543942.7	c.416-2644T>G		intron_variant		5	NM_001170633.2	P1
C12orf56	ENST00000333722.9	c.416-2644T>G		intron_variant		1
	ENST00000535684.6	n.324-55357A>C		intron_variant, non_coding_transcript_variant		2
C12orf56	ENST00000543259.1	c.377-2644T>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81887 AN: 151684 Hom.: 22638 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.540 AC: 81932 AN: 151802 Hom.: 22651 Cov.: 31 AF XY: 0.537 AC XY: 39833 AN XY: 74194

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.583

Alfa AF: 0.557 Hom.: 2865

Bravo AF: 0.545

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.0
Dann	Benign	0.73

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: rs7487873; hg19: chr12-64727456;