chr7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PM1PM4BP6_ModerateBS1BS2
The NM_014390.4(SND1):c.14_34dup(p.Ala5_Ser11dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,596,444 control chromosomes in the GnomAD database, including 162 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 19 hom., cov: 33)
Exomes 𝑓: 0.011 ( 143 hom. )
Consequence
SND1
NM_014390.4 inframe_insertion
NM_014390.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.70
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.
PM1
?
In a modified_residue N-acetylalanine (size 0) in uniprot entity SND1_HUMAN
PM4
?
Nonframeshift variant in NON repetitive region in NM_014390.4.
BP6
?
Variant 7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is Benign according to our data. Variant chr7-127652379-G-GTCCTCCGCGCAGAGCGGCGGC is described in ClinVar as [Benign]. Clinvar id is 718333.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00775 (1181/152306) while in subpopulation SAS AF= 0.0423 (204/4824). AF 95% confidence interval is 0.0375. There are 19 homozygotes in gnomad4. There are 591 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1181 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.14_34dup | p.Ala5_Ser11dup | inframe_insertion | 1/24 | ENST00000354725.8 | |
SND1 | XM_017011987.3 | c.14_34dup | p.Ala5_Ser11dup | inframe_insertion | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.14_34dup | p.Ala5_Ser11dup | inframe_insertion | 1/24 | 1 | NM_014390.4 | P1 | |
SND1 | ENST00000463020.1 | n.194_214dup | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00776 AC: 1181AN: 152188Hom.: 19 Cov.: 33
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GnomAD3 exomes AF: 0.00789 AC: 1706AN: 216140Hom.: 25 AF XY: 0.00900 AC XY: 1048AN XY: 116470
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GnomAD4 exome AF: 0.0105 AC: 15196AN: 1444138Hom.: 143 Cov.: 30 AF XY: 0.0112 AC XY: 8011AN XY: 716374
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GnomAD4 genome ? AF: 0.00775 AC: 1181AN: 152306Hom.: 19 Cov.: 33 AF XY: 0.00794 AC XY: 591AN XY: 74476
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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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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at