12-6943843-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP4

The NR_023317.1(RNU7-1):n.28C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.000652 in 888,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00062 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00066 (0 hom.)
• Consequence: RNU7-1 NR_023317.1 non_coding_transcript_exon
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 3.71

Genes affected

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

(HGNC:):

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-6943843-C-T is Pathogenic according to our data. Variant chr12-6943843-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1202611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RNU7-1	NR_023317.1	n.28C>T		non_coding_transcript_exon_variant	1/1
C12orf57	NM_001301834.1	c.-16+181C>T		intron_variant
C12orf57	NM_001301836.2	c.13+181C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNU7-1	ENST00000458811.1	n.28C>T		non_coding_transcript_exon_variant	1/1
	ENST00000607421.2	n.788G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.000618 AC: 94 AN: 152210 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000764

Gnomad OTH AF: 0.000956

GnomAD4 exome AF: 0.000659 AC: 485 AN: 736138 Hom.: 0 Cov.: 10 AF XY: 0.000663 AC XY: 245 AN XY: 369452

Gnomad4 AFR exome AF: 0.000590

Gnomad4 AMR exome AF: 0.000745

Gnomad4 ASJ exome AF: 0.000149

Gnomad4 EAS exome AF: 0.000321

Gnomad4 SAS exome AF: 0.000370

Gnomad4 FIN exome AF: 0.000258

Gnomad4 NFE exome AF: 0.000734

Gnomad4 OTH exome AF: 0.000548

GnomAD4 genome AF: 0.000617 AC: 94 AN: 152328 Hom.: 0 Cov.: 33 AF XY: 0.000752 AC XY: 56 AN XY: 74492

Gnomad4 AFR AF: 0.000722

Gnomad4 AMR AF: 0.000458

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000764

Gnomad4 OTH AF: 0.000946

Alfa AF: 0.000106 Hom.: 0

Bravo AF: 0.000593

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Aicardi-Goutieres syndrome 9 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 02, 2022	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 16, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Undiagnosed Diseases Network, NIH	Sep 06, 2022	- -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 26, 2022

Published functional studies demonstrate a damaging effect with severely reduced processing efficiency (Kolev and Steitz, 2006); This variant is associated with the following publications: (PMID: 33230297, 16547514) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
Cadd	Benign	19
Dann	Benign	0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs180837208; hg19: chr12-7053006;