Variant 12-6944186-CTAGTCAAGGCATAGGCTGCTGGCCTGGGG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_138425.4(C12orf57):c.52+26_52+54del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,613,066 control chromosomes in the GnomAD database, including 172 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.010 ( 12 hom., cov: 33)

Exomes 𝑓: 0.014 ( 160 hom. )

Consequence

C12orf57
NM_138425.4 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 2.27

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-6944186-CTAGTCAAGGCATAGGCTGCTGGCCTGGGG-C is Benign according to our data. Variant chr12-6944186-CTAGTCAAGGCATAGGCTGCTGGCCTGGGG-C is described in ClinVar as [Likely_benign]. Clinvar id is 210549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0103 (1569/152272) while in subpopulation NFE AF= 0.0155 (1054/68002). AF 95% confidence interval is 0.0147. There are 12 homozygotes in gnomad4. There are 738 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C12orf57	NM_138425.4 linkuse as main transcript	c.52+26_52+54del		intron_variant		ENST00000229281.6	NP_612434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C12orf57	ENST00000229281.6 linkuse as main transcript	c.52+26_52+54del		intron_variant		1	NM_138425.4	ENSP00000229281	P1
	ENST00000607421.2 linkuse as main transcript	n.416_444del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0103

AC:

1569

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00302

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0102

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.00577

Gnomad SAS

AF:

0.0134

Gnomad FIN

AF:

0.00339

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0155

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.0114

AC:

2874

AN:

251392

Hom.:

AF XY:

0.0121

AC XY:

1648

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.00234

Gnomad AMR exome

AF:

0.00506

Gnomad ASJ exome

AF:

0.0199

Gnomad EAS exome

AF:

0.00598

Gnomad SAS exome

AF:

0.0143

Gnomad FIN exome

AF:

0.00430

Gnomad NFE exome

AF:

0.0153

Gnomad OTH exome

AF:

0.0122

GnomAD4 exome

AF:

0.0142

AC:

20701

AN:

1460794

Hom.:

160

AF XY:

0.0142

AC XY:

10292

AN XY:

726724

show subpopulations

Gnomad4 AFR exome

AF:

0.00266

Gnomad4 AMR exome

AF:

0.00508

Gnomad4 ASJ exome

AF:

0.0217

Gnomad4 EAS exome

AF:

0.00899

Gnomad4 SAS exome

AF:

0.0133

Gnomad4 FIN exome

AF:

0.00449

Gnomad4 NFE exome

AF:

0.0156

Gnomad4 OTH exome

AF:

0.0123

GnomAD4 genome

AF:

0.0103

AC:

1569

AN:

152272

Hom.:

Cov.:

AF XY:

0.00991

AC XY:

738

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00301

Gnomad4 AMR

AF:

0.0102

Gnomad4 ASJ

AF:

0.0228

Gnomad4 EAS

AF:

0.00578

Gnomad4 SAS

AF:

0.0132

Gnomad4 FIN

AF:

0.00339

Gnomad4 NFE

AF:

0.0155

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0115

Hom.:

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 29, 2015

- -

Temtamy syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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