rs6488724

chr12-14879827-G-A

Variant summary

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

The ENST00000527783.1(C12orf60):n.76-19342G>A 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 0.396 in 151,996 control chromosomes in the GnomAD database, including 12,525 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 0.40 (12525 hom., cov: 32)
• Consequence: C12orf60 ENST00000527783.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf60	ENST00000527783.1	n.76-19342G>A		intron_variant, non_coding_transcript_variant		2
C12orf60	ENST00000533472.1	n.87-24180G>A		intron_variant, non_coding_transcript_variant		3
C12orf60	ENST00000648334.1	n.126-24180G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60175 AN: 151876 Hom.: 12495 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.396 AC: 60250 AN: 151996 Hom.: 12525 Cov.: 32 AF XY: 0.392 AC XY: 29148 AN XY: 74288

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.398

Alfa AF: 0.387 Hom.: 5972

Bravo AF: 0.403

Asia WGS AF: 0.296 AC: 1033 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.41
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6488724; hg19: chr12-15032761;