rs144346422
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005460.4(SNCAIP):āc.1725A>Gā(p.Lys575Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,614,082 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.00068 ( 0 hom., cov: 32)
Exomes š: 0.000063 ( 1 hom. )
Consequence
SNCAIP
NM_005460.4 synonymous
NM_005460.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.449
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 -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 5-122450572-A-G is Benign according to our data. Variant chr5-122450572-A-G is described in ClinVar as [Benign]. Clinvar id is 711930.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.449 with no splicing effect.
BS2
High AC in GnomAd4 at 104 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000670 AC: 102AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000235 AC: 59AN: 250588Hom.: 1 AF XY: 0.000140 AC XY: 19AN XY: 135714
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GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461816Hom.: 1 Cov.: 33 AF XY: 0.0000605 AC XY: 44AN XY: 727214
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GnomAD4 genome AF: 0.000683 AC: 104AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000766 AC XY: 57AN XY: 74458
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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
Dec 20, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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