7-127694891-A-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014390.4(SND1):āc.292A>Gā(p.Thr98Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000162 in 1,613,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000085 ( 0 hom., cov: 32)
Exomes š: 0.00017 ( 0 hom. )
Consequence
SND1
NM_014390.4 missense
NM_014390.4 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 6.32
Genes affected
SND1 (HGNC:30646): (staphylococcal nuclease and tudor domain containing 1) This gene encodes a transcriptional co-activator that interacts with the acidic domain of Epstein-Barr virus nuclear antigen 2 (EBNA 2), a transcriptional activator that is required for B-lymphocyte transformation. Other transcription factors that interact with this protein are signal transducers and activators of transcription, STATs. This protein is also thought to be essential for normal cell growth. A similar protein in mammals and other organisms is a component of the RNA-induced silencing complex (RISC). [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.12941483).
BS2
High AC in GnomAd4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.292A>G | p.Thr98Ala | missense_variant | 3/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.292A>G | p.Thr98Ala | missense_variant | 3/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.292A>G | p.Thr98Ala | missense_variant | 3/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000223 AC: 56AN: 250866Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135572
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GnomAD4 exome AF: 0.000170 AC: 249AN: 1461646Hom.: 0 Cov.: 30 AF XY: 0.000160 AC XY: 116AN XY: 727118
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GnomAD4 genome AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74360
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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 | Jun 18, 2021 | The c.292A>G (p.T98A) alteration is located in exon 3 (coding exon 3) of the SND1 gene. This alteration results from a A to G substitution at nucleotide position 292, causing the threonine (T) at amino acid position 98 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
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at