chr7-127704919-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014390.4(SND1):c.921C>T(p.Gly307=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00157 in 1,613,944 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0080 ( 17 hom., cov: 33)
Exomes 𝑓: 0.00090 ( 16 hom. )
Consequence
SND1
NM_014390.4 synonymous
NM_014390.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -5.06
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 7-127704919-C-T is Benign according to our data. Variant chr7-127704919-C-T is described in ClinVar as [Benign]. Clinvar id is 787864.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-5.06 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00796 (1211/152192) while in subpopulation AFR AF= 0.0271 (1123/41510). AF 95% confidence interval is 0.0257. There are 17 homozygotes in gnomad4. There are 571 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1204 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.921C>T | p.Gly307= | synonymous_variant | 8/24 | ENST00000354725.8 | |
SND1 | XM_017011987.3 | c.921C>T | p.Gly307= | synonymous_variant | 8/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.921C>T | p.Gly307= | synonymous_variant | 8/24 | 1 | NM_014390.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00792 AC: 1204AN: 152074Hom.: 17 Cov.: 33
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GnomAD3 exomes AF: 0.00214 AC: 538AN: 251158Hom.: 10 AF XY: 0.00152 AC XY: 206AN XY: 135724
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GnomAD4 exome AF: 0.000900 AC: 1315AN: 1461752Hom.: 16 Cov.: 30 AF XY: 0.000763 AC XY: 555AN XY: 727184
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GnomAD4 genome ? AF: 0.00796 AC: 1211AN: 152192Hom.: 17 Cov.: 33 AF XY: 0.00767 AC XY: 571AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at