Variant chr12-6943859-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NR_023317.1(RNU7-1):n.44C>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 0.341 in 936,706 control chromosomes in the GnomAD database, including 62,021 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.45 ( 18616 hom., cov: 33)

Exomes 𝑓: 0.32 ( 43405 hom. )

Consequence

RNU7-1
NR_023317.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.26

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 12-6943859-C-T is Benign according to our data. Variant chr12-6943859-C-T is described in ClinVar as [Benign]. Clinvar id is 1181108.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
RNU7-1	NR_023317.1 linkuse as main transcript	n.44C>T	non_coding_transcript_exon_variant	1/1
C12orf57	NM_001301834.1 linkuse as main transcript	c.-16+197C>T	intron_variant
C12orf57	NM_001301836.2 linkuse as main transcript	c.13+197C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNU7-1	ENST00000458811.1 linkuse as main transcript	n.44C>T		non_coding_transcript_exon_variant	1/1
	ENST00000607421.2 linkuse as main transcript	n.772G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67611

AN:

151960

Hom.:

18563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.453

GnomAD4 exome

AF:

0.320

AC:

251301

AN:

784628

Hom.:

43405

Cov.:

AF XY:

0.320

AC XY:

125680

AN XY:

392818

show subpopulations

Gnomad4 AFR exome

AF:

0.814

Gnomad4 AMR exome

AF:

0.369

Gnomad4 ASJ exome

AF:

0.315

Gnomad4 EAS exome

AF:

0.275

Gnomad4 SAS exome

AF:

0.339

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.305

Gnomad4 OTH exome

AF:

0.350

GnomAD4 genome

AF:

0.445

AC:

67721

AN:

152078

Hom.:

18616

Cov.:

AF XY:

0.438

AC XY:

32551

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.787

Gnomad4 AMR

AF:

0.403

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.306

Gnomad4 OTH

AF:

0.456

Alfa

AF:

0.239

Hom.:

807

Bravo

AF:

0.472

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 61% of patients studied by a panel of primary immunodeficiencies. Number of patients: 58. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

0.30

DANN

Benign

0.61

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