12-14885985-A-G

Position:

• chr12-14885985-A-G

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The ENST00000527783.1(C12orf60):​n.76-13184A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 623,554 control chromosomes in the GnomAD database, including 14,924 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (2554 hom., cov: 32)
  • Exomes 𝑓: 0.22 (12370 hom.)
• Consequence: C12orf60 ENST00000527783.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.49

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP6: Variant 12-14885985-A-G is Benign according to our data. Variant chr12-14885985-A-G is described in ClinVar as [Benign]. Clinvar id is 1166186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf60	ENST00000527783.1	n.76-13184A>G		intron_variant, non_coding_transcript_variant		2
C12orf60	ENST00000533472.1	n.87-18022A>G		intron_variant, non_coding_transcript_variant		3
C12orf60	ENST00000543822.1	n.91+179A>G		intron_variant, non_coding_transcript_variant		3
C12orf60	ENST00000648334.1	n.126-18022A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23987 AN: 152132 Hom.: 2552 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.184

GnomAD4 exome AF: 0.219 AC: 103308 AN: 471304 Hom.: 12370 AF XY: 0.227 AC XY: 57308 AN XY: 251968

Gnomad4 AFR exome AF: 0.0378

Gnomad4 AMR exome AF: 0.0993

Gnomad4 ASJ exome AF: 0.271

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.328

Gnomad4 FIN exome AF: 0.176

Gnomad4 NFE exome AF: 0.207

Gnomad4 OTH exome AF: 0.213

GnomAD4 genome AF: 0.158 AC: 23981 AN: 152250 Hom.: 2554 Cov.: 32 AF XY: 0.158 AC XY: 11756 AN XY: 74432

Gnomad4 AFR AF: 0.0360

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.329

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.181

Alfa AF: 0.189 Hom.: 1676

Bravo AF: 0.147

Asia WGS AF: 0.269 AC: 934 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	This variant is associated with the following publications: (PMID: 11073842, 11425864) -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 02, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Benign	0.88

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1800802; hg19: chr12-15038919;