5-122422977-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_005460.4(SNCAIP):c.240G>A(p.Ser80=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000226 in 1,614,128 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00025 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 2 hom. )
Consequence
SNCAIP
NM_005460.4 synonymous
NM_005460.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.130
Genes affected
SNCAIP (HGNC:11139): (synuclein alpha interacting protein) This gene encodes a protein containing several protein-protein interaction domains, including ankyrin-like repeats, a coiled-coil domain, and an ATP/GTP-binding motif. The encoded protein interacts with alpha-synuclein in neuronal tissue and may play a role in the formation of cytoplasmic inclusions and neurodegeneration. A mutation in this gene has been associated with Parkinson's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 5-122422977-G-A is Benign according to our data. Variant chr5-122422977-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 753378.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.13 with no splicing effect.
BS2
High AC in GnomAd4 at 38 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNCAIP | NM_005460.4 | c.240G>A | p.Ser80= | synonymous_variant | 4/11 | ENST00000261368.13 | NP_005451.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNCAIP | ENST00000261368.13 | c.240G>A | p.Ser80= | synonymous_variant | 4/11 | 1 | NM_005460.4 | ENSP00000261368 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152136Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000107 AC: 27AN: 251190Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135748
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GnomAD4 exome AF: 0.000223 AC: 326AN: 1461874Hom.: 2 Cov.: 32 AF XY: 0.000216 AC XY: 157AN XY: 727242
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GnomAD4 genome AF: 0.000250 AC: 38AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74448
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 08, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at