12-14822787-C-T

Position:

• chr12-14822787-C-T

Variant summary

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

The NM_175874.4(C12orf60):​c.-24-125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 687,864 control chromosomes in the GnomAD database, including 111,721 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 0.59 (26590 hom., cov: 32)
  • Exomes 𝑓: 0.56 (85131 hom.)
• Consequence: C12orf60 NM_175874.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

C12orf60 (HGNC:28726): (chromosome 12 open reading frame 60)

C12orf60 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf60	NM_175874.4	c.-24-125C>T		intron_variant		ENST00000330828.3	NP_787070.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf60	ENST00000330828.3	c.-24-125C>T		intron_variant		1	NM_175874.4	ENSP00000331691.2
C12orf60	ENST00000527783.1	n.75+19036C>T		intron_variant		2
C12orf60	ENST00000533472.1	n.86+19036C>T		intron_variant		3
C12orf60	ENST00000648334.1	n.84-6851C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89107 AN: 151982 Hom.: 26533 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.585

GnomAD4 exome AF: 0.557 AC: 298382 AN: 535764 Hom.: 85131 AF XY: 0.558 AC XY: 153382 AN XY: 274690

Gnomad4 AFR exome AF: 0.630

Gnomad4 AMR exome AF: 0.650

Gnomad4 ASJ exome AF: 0.578

Gnomad4 EAS exome AF: 0.271

Gnomad4 SAS exome AF: 0.600

Gnomad4 FIN exome AF: 0.540

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.560

GnomAD4 genome AF: 0.587 AC: 89226 AN: 152100 Hom.: 26590 Cov.: 32 AF XY: 0.584 AC XY: 43429 AN XY: 74332

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.587

Alfa AF: 0.585 Hom.: 12489

Bravo AF: 0.595

Asia WGS AF: 0.509 AC: 1764 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.67

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: rs11610238; hg19: chr12-14975721; COSMIC: COSV57451808; COSMIC: COSV57451808;