NM_175874.4:c.-24-125C>T

Variant names:

• chr12-14822787-C-T
• rs11610238
• NM_175874.4:c.-24-125C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

Genes affected

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

ENSG00000256339 (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 (AMR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175874.4. 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
	C12orf60	NM_175874.4	MANE Select	c.-24-125C>T		intron	N/A	NP_787070.2	Q5U649

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf60	ENST00000330828.3	TSL:1 MANE Select	c.-24-125C>T		intron	N/A	ENSP00000331691.2	Q5U649
	C12orf60	ENST00000857839.1		c.-24-125C>T		intron	N/A	ENSP00000527898.1
	C12orf60	ENST00000857840.1		c.-24-125C>T		intron	N/A	ENSP00000527899.1

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

African (AFR) AF: 0.630 AC: 8881 AN: 14100

American (AMR) AF: 0.650 AC: 9848 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 7710 AN: 13350

East Asian (EAS) AF: 0.271 AC: 8342 AN: 30828

South Asian (SAS) AF: 0.600 AC: 19439 AN: 32424

European-Finnish (FIN) AF: 0.540 AC: 17080 AN: 31620

Middle Eastern (MID) AF: 0.607 AC: 1252 AN: 2064

European-Non Finnish (NFE) AF: 0.571 AC: 210219 AN: 368330

Other (OTH) AF: 0.560 AC: 15611 AN: 27888

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

African (AFR) AF: 0.635 AC: 26339 AN: 41494

American (AMR) AF: 0.644 AC: 9850 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1993 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1337 AN: 5178

South Asian (SAS) AF: 0.589 AC: 2840 AN: 4822

European-Finnish (FIN) AF: 0.539 AC: 5695 AN: 10562

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39126 AN: 67966

Other (OTH) AF: 0.587 AC: 1238 AN: 2108

Alfa AF: 0.585 Hom.: 13978

Bravo AF: 0.595

Asia WGS AF: 0.509 AC: 1764 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.25
DANN	Benign	0.67
PhyloP100		-1.4
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: rs11610238; hg19: chr12-14975721; COSMIC: COSV57451808; COSMIC: COSV57451808;