6-157921522-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_016224.5(SNX9):c.950-9C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,609,356 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 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00024 ( 0 hom. )
Consequence
SNX9
NM_016224.5 splice_polypyrimidine_tract, intron
NM_016224.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00001756
2
Clinical Significance
Conservation
PhyloP100: -1.22
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.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
Variant 6-157921522-C-T is Benign according to our data. Variant chr6-157921522-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 742459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNX9 | NM_016224.5 | c.950-9C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000392185.8 | NP_057308.1 | |||
SNX9 | XM_011535886.4 | c.668-9C>T | splice_polypyrimidine_tract_variant, intron_variant | XP_011534188.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNX9 | ENST00000392185.8 | c.950-9C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016224.5 | ENSP00000376024 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000198 AC: 30AN: 151556Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000132 AC: 33AN: 249610Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 134984
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GnomAD4 exome AF: 0.000244 AC: 355AN: 1457800Hom.: 0 Cov.: 30 AF XY: 0.000239 AC XY: 173AN XY: 725012
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GnomAD4 genome AF: 0.000198 AC: 30AN: 151556Hom.: 0 Cov.: 32 AF XY: 0.000176 AC XY: 13AN XY: 73932
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 31, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at