chr7-127686728-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014390.4(SND1):c.194C>T(p.Ala65Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,614,182 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0010 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
SND1
NM_014390.4 missense
NM_014390.4 missense
Scores
2
17
Clinical Significance
Conservation
PhyloP100: 1.48
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 Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005766958).
BS2
High AC in GnomAd4 at 156 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.194C>T | p.Ala65Val | missense_variant | 2/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.194C>T | p.Ala65Val | missense_variant | 2/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.194C>T | p.Ala65Val | missense_variant | 2/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 | |
SND1 | ENST00000461056.5 | n.337C>T | non_coding_transcript_exon_variant | 2/4 | 4 | |||||
SND1 | ENST00000463020.1 | n.374C>T | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
SND1 | ENST00000468621.5 | n.209C>T | non_coding_transcript_exon_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 156AN: 152222Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000832 AC: 209AN: 251350Hom.: 0 AF XY: 0.000847 AC XY: 115AN XY: 135836
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GnomAD4 exome AF: 0.00108 AC: 1579AN: 1461842Hom.: 2 Cov.: 30 AF XY: 0.00108 AC XY: 788AN XY: 727216
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GnomAD4 genome AF: 0.00102 AC: 156AN: 152340Hom.: 1 Cov.: 33 AF XY: 0.000980 AC XY: 73AN XY: 74494
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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 | May 04, 2022 | The c.194C>T (p.A65V) alteration is located in exon 2 (coding exon 2) of the SND1 gene. This alteration results from a C to T substitution at nucleotide position 194, causing the alanine (A) at amino acid position 65 to be replaced by a valine (V). 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
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
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