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12-6943875-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NR_023317.1(RNU7-1):n.60C>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 0.00578 in 974,422 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0088 ( 7 hom., cov: 33)
Exomes 𝑓: 0.0052 ( 24 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: 2.51
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 -14 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 12-6943875-C-T is Benign according to our data. Variant chr12-6943875-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1301145.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00876 (1334/152252) while in subpopulation AFR AF= 0.018 (747/41552). AF 95% confidence interval is 0.0169. There are 7 homozygotes in gnomad4. There are 620 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNU7-1NR_023317.1 linkuse as main transcriptn.60C>T non_coding_transcript_exon_variant 1/1
C12orf57NM_001301834.1 linkuse as main transcriptc.-16+213C>T intron_variant
C12orf57NM_001301836.2 linkuse as main transcriptc.13+213C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNU7-1ENST00000458811.1 linkuse as main transcriptn.60C>T non_coding_transcript_exon_variant 1/1
ENST00000607421.2 linkuse as main transcriptn.756G>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00876
AC:
1333
AN:
152130
Hom.:
7
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0180
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00589
Gnomad ASJ
AF:
0.00721
Gnomad EAS
AF:
0.00654
Gnomad SAS
AF:
0.00746
Gnomad FIN
AF:
0.000943
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00550
Gnomad OTH
AF:
0.00814
GnomAD4 exome
AF:
0.00523
AC:
4302
AN:
822170
Hom.:
24
Cov.:
11
AF XY:
0.00531
AC XY:
2186
AN XY:
411622
show subpopulations
Gnomad4 AFR exome
AF:
0.0166
Gnomad4 AMR exome
AF:
0.00461
Gnomad4 ASJ exome
AF:
0.00633
Gnomad4 EAS exome
AF:
0.00645
Gnomad4 SAS exome
AF:
0.00732
Gnomad4 FIN exome
AF:
0.00119
Gnomad4 NFE exome
AF:
0.00479
Gnomad4 OTH exome
AF:
0.00578
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00876
AC:
1334
AN:
152252
Hom.:
7
Cov.:
33
AF XY:
0.00833
AC XY:
620
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.0180
Gnomad4 AMR
AF:
0.00588
Gnomad4 ASJ
AF:
0.00721
Gnomad4 EAS
AF:
0.00656
Gnomad4 SAS
AF:
0.00746
Gnomad4 FIN
AF:
0.000943
Gnomad4 NFE
AF:
0.00550
Gnomad4 OTH
AF:
0.00806
Alfa
AF:
0.00414
Hom.:
2
Bravo
AF:
0.00976

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 testingGeneDxApr 02, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
12
Dann
Benign
0.72
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: rs115355876; hg19: chr12-7053038; API