chr12-6943859-C-T

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

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]
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 -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 HGVSp Effect #exon/exons MANE UniProt
RNU7-1NR_023317.1 linkuse as main transcriptn.44C>T non_coding_transcript_exon_variant 1/1
C12orf57NM_001301834.1 linkuse as main transcriptc.-16+197C>T intron_variant
C12orf57NM_001301836.2 linkuse as main transcriptc.13+197C>T intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes
AF:
0.445
AC:
67611
AN:
151960
Hom.:
18563
Cov.:
33
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.:
10
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.:
33
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:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingUnidad de Genómica Garrahan, Hospital de Pediatría GarrahanJan 24, 2024This 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. -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxNov 10, 2018- -

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.

Other links and lift over

dbSNP: rs7965269; hg19: chr12-7053022; COSMIC: COSV57547057; COSMIC: COSV57547057; API