12-14813670-C-T

Variant names:

• chr12-14813670-C-T
• rs4764124
• NM_175874.4:c.-24-9242C>T

Variant summary

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

The NM_175874.4(C12orf60):​c.-24-9242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,886 control chromosomes in the GnomAD database, including 20,224 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 0.51 (20224 hom., cov: 31)
• Consequence: C12orf60 NM_175874.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

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

SMCO3 (HGNC:34401): (single-pass membrane protein with coiled-coil domains 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf60	NM_175874.4	c.-24-9242C>T		intron_variant	Intron 1 of 1	ENST00000330828.3	NP_787070.2
SMCO3	NM_001013698.2	c.-17+456G>A		intron_variant	Intron 1 of 1	ENST00000316048.2	NP_001013720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf60	ENST00000330828.3	c.-24-9242C>T		intron_variant	Intron 1 of 1	1	NM_175874.4	ENSP00000331691.2
SMCO3	ENST00000316048.2	c.-17+456G>A		intron_variant	Intron 1 of 1	1	NM_001013698.2	ENSP00000381895.1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77335 AN: 151768 Hom.: 20167 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.510 AC: 77454 AN: 151886 Hom.: 20224 Cov.: 31 AF XY: 0.509 AC XY: 37744 AN XY: 74210

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.501

Alfa AF: 0.461 Hom.: 7158

Bravo AF: 0.523

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.035
DANN	Benign	0.46

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: rs4764124; hg19: chr12-14966604;