Genetic Variant C12orf57:c.-255C>T (chr12-6943867-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001301834.1(C12orf57):c.-16+205C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0181 in 939,128 control chromosomes in the GnomAD database, including 186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 20 hom., cov: 33)

Exomes 𝑓: 0.019 ( 166 hom. )

Consequence

C12orf57
NM_001301834.1 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.752

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]

C12orf57 links:

RNU7-1 (HGNC:34033): (RNA, U7 small nuclear 1) Implicated in Aicardi-Goutieres syndrome. [provided by Alliance of Genome Resources, Apr 2022]

RNU7-1 links:

ENSG00000272173 (HGNC:):

ENSG00000272173 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 12-6943867-C-T is Benign according to our data. Variant chr12-6943867-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1301050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0154 (2344/152260) while in subpopulation AMR AF= 0.0223 (341/15294). AF 95% confidence interval is 0.0203. There are 20 homozygotes in gnomad4. There are 1077 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf57	NM_138425.4 link	c.-255C>T		upstream_gene_variant		ENST00000229281.6	NP_612434.1	Q99622

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf57	ENST00000229281.6 link	c.-255C>T		upstream_gene_variant		1	NM_138425.4	ENSP00000229281.5		Q99622

Frequencies

GnomAD3 genomes

AF:

0.0154

AC:

2343

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00956

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.00643

Gnomad FIN

AF:

0.00755

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0191

Gnomad OTH

AF:

0.0211

GnomAD4 exome

AF:

0.0186

AC:

14674

AN:

786868

Hom.:

166

Cov.:

AF XY:

0.0187

AC XY:

7373

AN XY:

394480

show subpopulations

Gnomad4 AFR exome

AF:

0.00838

Gnomad4 AMR exome

AF:

0.0228

Gnomad4 ASJ exome

AF:

0.0299

Gnomad4 EAS exome

AF:

0.000931

Gnomad4 SAS exome

AF:

0.00909

Gnomad4 FIN exome

AF:

0.00767

Gnomad4 NFE exome

AF:

0.0208

Gnomad4 OTH exome

AF:

0.0170

GnomAD4 genome

AF:

0.0154

AC:

2344

AN:

152260

Hom.:

Cov.:

AF XY:

0.0145

AC XY:

1077

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00953

Gnomad4 AMR

AF:

0.0223

Gnomad4 ASJ

AF:

0.0334

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.00644

Gnomad4 FIN

AF:

0.00755

Gnomad4 NFE

AF:

0.0191

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.00429

Hom.:

Bravo

AF:

0.0164

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 29, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

0.058

DANN

Benign

0.72

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over