Variant 12-6943866-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NR_023317.1(RNU7-1):n.51C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0038 in 934,242 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0055 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0035 ( 4 hom. )

Consequence

RNU7-1
NR_023317.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts P:1B:2

Conservation

PhyloP100: 0.538

Variant links:

Genes affected

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:

(HGNC:):

links:

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP6

Variant 12-6943866-C-T is Benign according to our data. Variant chr12-6943866-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1202613.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
RNU7-1	NR_023317.1 linkuse as main transcript	n.51C>T	non_coding_transcript_exon_variant	1/1
C12orf57	NM_001301834.1 linkuse as main transcript	c.-16+204C>T	intron_variant
C12orf57	NM_001301836.2 linkuse as main transcript	c.13+204C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNU7-1	ENST00000458811.1 linkuse as main transcript	n.51C>T		non_coding_transcript_exon_variant	1/1
	ENST00000607421.2 linkuse as main transcript	n.765G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00545

AC:

830

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0126

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00308

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00323

Gnomad OTH

AF:

0.00478

GnomAD4 exome

AF:

0.00347

AC:

2711

AN:

781944

Hom.:

Cov.:

AF XY:

0.00335

AC XY:

1313

AN XY:

391962

show subpopulations

Gnomad4 AFR exome

AF:

0.0133

Gnomad4 AMR exome

AF:

0.00272

Gnomad4 ASJ exome

AF:

0.00456

Gnomad4 EAS exome

AF:

0.00253

Gnomad4 SAS exome

AF:

0.000707

Gnomad4 FIN exome

AF:

0.000444

Gnomad4 NFE exome

AF:

0.00355

Gnomad4 OTH exome

AF:

0.00408

GnomAD4 genome

AF:

0.00551

AC:

839

AN:

152298

Hom.:

Cov.:

AF XY:

0.00526

AC XY:

392

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0128

Gnomad4 AMR

AF:

0.00307

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00323

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.000160

Hom.:

Bravo

AF:

0.00641

ClinVar

Significance: Benign/Likely benign

Submissions summary: Pathogenic:1Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 07, 2021	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	C12orf57: BS1, BS2; RNU7-1: BS1, BS2 -

Aicardi-Goutieres syndrome 9

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Aug 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.2

DANN

Benign

0.70

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