rs6488724

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.383
Variant links:
Genes affected
C12orf60 (HGNC:28726): (chromosome 12 open reading frame 60)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C12orf60ENST00000527783.1 linkn.76-19342G>A intron_variant Intron 1 of 3 2
C12orf60ENST00000533472.1 linkn.87-24180G>A intron_variant Intron 1 of 1 3
C12orf60ENST00000648334.1 linkn.126-24180G>A intron_variant Intron 2 of 2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6488724; hg19: chr12-15032761; API