chr12-6943845-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001301834.1(C12orf57):​c.-16+183A>T variant causes a intron change. The variant allele was found at a frequency of 0.0000027 in 741,662 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

C12orf57
NM_001301834.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.38
Variant links:
Genes affected
C12orf57 (HGNC:29521): (chromosome 12 open reading frame 57) This gene is ubiquitously expressed in human tissues. It is required for development of the human corpus callosum. Mutations in this gene are associated with Temtamy syndrome (TEMTYS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
RNU7-1 (HGNC:34033): (RNA, U7 small nuclear 1) Implicated in Aicardi-Goutieres syndrome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
C12orf57NM_001301834.1 linkc.-16+183A>T intron_variant Intron 1 of 3 NP_001288763.1 Q99622
C12orf57NM_001301836.2 linkc.13+183A>T intron_variant Intron 1 of 2 NP_001288765.1
RNU7-1NR_023317.1 linkn.30A>T non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C12orf57ENST00000544681 linkc.-277A>T 5_prime_UTR_premature_start_codon_gain_variant Exon 1 of 2 2 ENSP00000475422.1 U3KQ07
C12orf57ENST00000537087 linkc.-277A>T 5_prime_UTR_premature_start_codon_gain_variant Exon 1 of 3 2 ENSP00000440937.1 F5GXW5
C12orf57ENST00000544681 linkc.-277A>T 5_prime_UTR_variant Exon 1 of 2 2 ENSP00000475422.1 U3KQ07

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000270
AC:
2
AN:
741662
Hom.:
0
Cov.:
10
AF XY:
0.00
AC XY:
0
AN XY:
372056
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000355
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.34
CADD
Benign
15
DANN
Benign
0.85
RBP_binding_hub_radar
1.1
RBP_regulation_power_radar
2.3

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: rs781842057; hg19: chr12-7053008; API