chr9-15458046-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001039697.2(SNAPC3):c.1067T>C(p.Val356Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,430,442 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000016 ( 1 hom. )
Consequence
SNAPC3
NM_001039697.2 missense
NM_001039697.2 missense
Scores
2
10
6
Clinical Significance
Conservation
PhyloP100: 7.22
Genes affected
SNAPC3 (HGNC:11136): (small nuclear RNA activating complex polypeptide 3) Predicted to enable RNA polymerase III type 3 promoter sequence-specific DNA binding activity and bent DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and core promoter sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAPC3 | NM_001039697.2 | c.1067T>C | p.Val356Ala | missense_variant | 8/9 | ENST00000380821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC3 | ENST00000380821.8 | c.1067T>C | p.Val356Ala | missense_variant | 8/9 | 1 | NM_001039697.2 | P1 | |
SNAPC3 | ENST00000610884.4 | c.1067T>C | p.Val356Ala | missense_variant | 8/12 | 1 | P1 | ||
SNAPC3 | ENST00000467062.5 | c.1067T>C | p.Val356Ala | missense_variant, NMD_transcript_variant | 8/12 | 1 | |||
SNAPC3 | ENST00000490969.5 | c.1067T>C | p.Val356Ala | missense_variant, NMD_transcript_variant | 8/10 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1430442Hom.: 1 Cov.: 27 AF XY: 0.0000141 AC XY: 10AN XY: 711604
GnomAD4 exome
AF:
AC:
23
AN:
1430442
Hom.:
Cov.:
27
AF XY:
AC XY:
10
AN XY:
711604
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.1067T>C (p.V356A) alteration is located in exon 8 (coding exon 8) of the SNAPC3 gene. This alteration results from a T to C substitution at nucleotide position 1067, causing the valine (V) at amino acid position 356 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;.
REVEL
Uncertain
Sift
Benign
D;.
Sift4G
Benign
T;T
Polyphen
P;P
Vest4
MutPred
Loss of sheet (P = 0.0357);Loss of sheet (P = 0.0357);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at