chr6-157901963-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_016224.5(SNX9):c.538G>A(p.Asp180Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,460 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0074 ( 7 hom., cov: 31)
Exomes 𝑓: 0.011 ( 127 hom. )
Consequence
SNX9
NM_016224.5 missense
NM_016224.5 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 8.72
Genes affected
SNX9 (HGNC:14973): (sorting nexin 9) This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004186243).
BP6
Variant 6-157901963-G-A is Benign according to our data. Variant chr6-157901963-G-A is described in ClinVar as [Benign]. Clinvar id is 790318.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 7 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX9 | NM_016224.5 | c.538G>A | p.Asp180Asn | missense_variant | 6/18 | ENST00000392185.8 | NP_057308.1 | |
SNX9 | XM_011535886.4 | c.256G>A | p.Asp86Asn | missense_variant | 3/15 | XP_011534188.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNX9 | ENST00000392185.8 | c.538G>A | p.Asp180Asn | missense_variant | 6/18 | 1 | NM_016224.5 | ENSP00000376024 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00746 AC: 1131AN: 151580Hom.: 7 Cov.: 31
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GnomAD3 exomes AF: 0.00830 AC: 2085AN: 251310Hom.: 19 AF XY: 0.00896 AC XY: 1217AN XY: 135850
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GnomAD4 exome AF: 0.0112 AC: 16343AN: 1461770Hom.: 127 Cov.: 34 AF XY: 0.0112 AC XY: 8129AN XY: 727206
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GnomAD4 genome AF: 0.00745 AC: 1130AN: 151690Hom.: 7 Cov.: 31 AF XY: 0.00726 AC XY: 538AN XY: 74118
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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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 16, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
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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