rs3812565
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_003086.4(SNAPC4):āc.3777A>Gā(p.Leu1259=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 1,576,956 control chromosomes in the GnomAD database, including 115,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.36 ( 10086 hom., cov: 33)
Exomes š: 0.38 ( 105757 hom. )
Consequence
SNAPC4
NM_003086.4 synonymous
NM_003086.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.79
Genes affected
SNAPC4 (HGNC:11137): (small nuclear RNA activating complex polypeptide 4) This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [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=-0.9).
BP6
?
Variant 9-136378050-T-C is Benign according to our data. Variant chr9-136378050-T-C is described in ClinVar as [Benign]. Clinvar id is 402490.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.79 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAPC4 | NM_003086.4 | c.3777A>G | p.Leu1259= | synonymous_variant | 22/24 | ENST00000684778.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC4 | ENST00000684778.1 | c.3777A>G | p.Leu1259= | synonymous_variant | 22/24 | NM_003086.4 | P1 | ||
SNAPC4 | ENST00000298532.2 | c.3777A>G | p.Leu1259= | synonymous_variant | 21/23 | 1 | P1 | ||
SNAPC4 | ENST00000637388.2 | c.3777A>G | p.Leu1259= | synonymous_variant | 22/24 | 5 | P1 | ||
SNAPC4 | ENST00000689006.1 | c.*2990A>G | 3_prime_UTR_variant, NMD_transcript_variant | 22/24 |
Frequencies
GnomAD3 genomes ? AF: 0.360 AC: 54503AN: 151404Hom.: 10057 Cov.: 33
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GnomAD3 exomes AF: 0.372 AC: 68165AN: 183368Hom.: 13457 AF XY: 0.360 AC XY: 36634AN XY: 101660
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GnomAD4 exome AF: 0.380 AC: 542361AN: 1425434Hom.: 105757 Cov.: 46 AF XY: 0.376 AC XY: 265730AN XY: 706510
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GnomAD4 genome ? AF: 0.360 AC: 54584AN: 151522Hom.: 10086 Cov.: 33 AF XY: 0.358 AC XY: 26489AN XY: 74026
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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