7-127652388-G-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_014390.4(SND1):āc.15G>Cā(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,598,812 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00075 ( 1 hom., cov: 33)
Exomes š: 0.00065 ( 5 hom. )
Consequence
SND1
NM_014390.4 synonymous
NM_014390.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.16
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=-0.32).
BP6
Variant 7-127652388-G-C is Benign according to our data. Variant chr7-127652388-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 726681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.16 with no splicing effect.
BS2
High AC in GnomAd4 at 115 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SND1 | NM_014390.4 | c.15G>C | p.Ala5= | synonymous_variant | 1/24 | ENST00000354725.8 | NP_055205.2 | |
SND1 | XM_017011987.3 | c.15G>C | p.Ala5= | synonymous_variant | 1/17 | XP_016867476.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SND1 | ENST00000354725.8 | c.15G>C | p.Ala5= | synonymous_variant | 1/24 | 1 | NM_014390.4 | ENSP00000346762 | P1 | |
SND1 | ENST00000463020.1 | n.195G>C | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000756 AC: 115AN: 152210Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000911 AC: 200AN: 219532Hom.: 2 AF XY: 0.00104 AC XY: 124AN XY: 118786
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GnomAD4 exome AF: 0.000646 AC: 935AN: 1446484Hom.: 5 Cov.: 30 AF XY: 0.000709 AC XY: 509AN XY: 717872
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GnomAD4 genome AF: 0.000755 AC: 115AN: 152328Hom.: 1 Cov.: 33 AF XY: 0.000685 AC XY: 51AN XY: 74492
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 23, 2018 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at