chr12-6943864-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_023317.1(RNU7-1):​n.49T>C 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 0.00193 in 937,242 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 3 hom. )

Consequence

RNU7-1
NR_023317.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.89
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
Variant 12-6943864-T-C is Benign according to our data. Variant chr12-6943864-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3024660.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNU7-1NR_023317.1 linkuse as main transcriptn.49T>C non_coding_transcript_exon_variant 1/1
C12orf57NM_001301834.1 linkuse as main transcriptc.-16+202T>C intron_variant
C12orf57NM_001301836.2 linkuse as main transcriptc.13+202T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNU7-1ENST00000458811.1 linkuse as main transcriptn.49T>C non_coding_transcript_exon_variant 1/1
ENST00000607421.2 linkuse as main transcriptn.767A>G non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.00352
AC:
536
AN:
152224
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00695
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.00288
Gnomad ASJ
AF:
0.00490
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00103
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00247
Gnomad OTH
AF:
0.00239
GnomAD4 exome
AF:
0.00162
AC:
1272
AN:
784900
Hom.:
3
Cov.:
10
AF XY:
0.00153
AC XY:
602
AN XY:
393746
show subpopulations
Gnomad4 AFR exome
AF:
0.00543
Gnomad4 AMR exome
AF:
0.00154
Gnomad4 ASJ exome
AF:
0.00284
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000574
Gnomad4 FIN exome
AF:
0.000177
Gnomad4 NFE exome
AF:
0.00174
Gnomad4 OTH exome
AF:
0.00178
GnomAD4 genome
AF:
0.00352
AC:
536
AN:
152342
Hom.:
2
Cov.:
33
AF XY:
0.00336
AC XY:
250
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.00693
Gnomad4 AMR
AF:
0.00288
Gnomad4 ASJ
AF:
0.00490
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00103
Gnomad4 NFE
AF:
0.00247
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00190
Hom.:
1
Bravo
AF:
0.00356

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2024RNU7-1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.63
CADD
Benign
0.0010
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.

Other links and lift over

dbSNP: rs145994149; hg19: chr12-7053027; API