rs778371
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394206.1(SNORC):c.*2043A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 158,708 control chromosomes in the GnomAD database, including 5,825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.27 ( 5615 hom., cov: 33)
Exomes 𝑓: 0.23 ( 210 hom. )
Consequence
SNORC
NM_001394206.1 3_prime_UTR
NM_001394206.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.114
Genes affected
SNORC (HGNC:33763): (secondary ossification center associated regulator of chondrocyte maturation) Predicted to be involved in cartilage development. Predicted to be located in collagen-containing extracellular matrix; cytoplasm; and extracellular region. Predicted to be integral component of membrane. Predicted to be active in cell periphery. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNORC | NM_001394206.1 | c.*2043A>G | 3_prime_UTR_variant | 3/3 | ENST00000331342.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNORC | ENST00000331342.5 | c.*2043A>G | 3_prime_UTR_variant | 3/3 | 1 | NM_001394206.1 | P1 | ||
SNORC | ENST00000467665.1 | n.2477A>G | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
SNORC | ENST00000481155.1 | n.404-53A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.266 AC: 40494AN: 151954Hom.: 5606 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
40494
AN:
151954
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.232 AC: 1539AN: 6636Hom.: 210 Cov.: 0 AF XY: 0.241 AC XY: 855AN XY: 3542
GnomAD4 exome
AF:
AC:
1539
AN:
6636
Hom.:
Cov.:
0
AF XY:
AC XY:
855
AN XY:
3542
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.267 AC: 40528AN: 152072Hom.: 5615 Cov.: 33 AF XY: 0.263 AC XY: 19515AN XY: 74330
GnomAD4 genome
?
AF:
AC:
40528
AN:
152072
Hom.:
Cov.:
33
AF XY:
AC XY:
19515
AN XY:
74330
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
389
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at