rs6488724

Variant names:

• chr12-14879827-G-A
• rs6488724
• ENST00000527783.1:n.76-19342G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527783.1(C12orf60):​n.76-19342G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf60	ENST00000527783.1	n.76-19342G>A		intron_variant	Intron 1 of 3	2
C12orf60	ENST00000533472.1	n.87-24180G>A		intron_variant	Intron 1 of 1	3
C12orf60	ENST00000648334.1	n.126-24180G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.467 AC: 19326 AN: 41422

American (AMR) AF: 0.395 AC: 6042 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3470

East Asian (EAS) AF: 0.121 AC: 626 AN: 5178

South Asian (SAS) AF: 0.427 AC: 2059 AN: 4824

European-Finnish (FIN) AF: 0.309 AC: 3264 AN: 10548

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26183 AN: 67964

Other (OTH) AF: 0.398 AC: 839 AN: 2106

Alfa AF: 0.388 Hom.: 6639

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6488724; hg19: chr12-15032761;