15-41851139-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016642.4(SPTBN5):c.10755C>T(p.Ser3585=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000067 in 1,613,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000070 ( 0 hom. )
Consequence
SPTBN5
NM_016642.4 synonymous
NM_016642.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.574
Genes affected
SPTBN5 (HGNC:15680): (spectrin beta, non-erythrocytic 5) Enables several functions, including cytoskeletal protein binding activity; dynein intermediate chain binding activity; and identical protein binding activity. Acts upstream of or within Golgi organization and lysosomal transport. Located in cytoplasm; photoreceptor connecting cilium; and photoreceptor disc membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 15-41851139-G-A is Benign according to our data. Variant chr15-41851139-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3057542.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.574 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTBN5 | NM_016642.4 | c.10755C>T | p.Ser3585= | synonymous_variant | 65/68 | ENST00000320955.8 | |
SPTBN5 | XM_017022299.2 | c.10935C>T | p.Ser3645= | synonymous_variant | 63/66 | ||
SPTBN5 | XM_017022302.2 | c.8112C>T | p.Ser2704= | synonymous_variant | 51/54 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTBN5 | ENST00000320955.8 | c.10755C>T | p.Ser3585= | synonymous_variant | 65/68 | 1 | NM_016642.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247206Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134530
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GnomAD4 exome AF: 0.0000698 AC: 102AN: 1460810Hom.: 0 Cov.: 36 AF XY: 0.0000661 AC XY: 48AN XY: 726642
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GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SPTBN5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 10, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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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