chr16-12048457-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_032167.5(SNX29):c.585C>G(p.Leu195=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000488 in 1,613,944 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 3 hom., cov: 31)
Exomes 𝑓: 0.00051 ( 14 hom. )
Consequence
SNX29
NM_032167.5 synonymous
NM_032167.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.254
Genes affected
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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=-0.46).
BP6
?
Variant 16-12048457-C-G is Benign according to our data. Variant chr16-12048457-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2646233.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.254 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNX29 | NM_032167.5 | c.585C>G | p.Leu195= | synonymous_variant | 7/21 | ENST00000566228.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNX29 | ENST00000566228.6 | c.585C>G | p.Leu195= | synonymous_variant | 7/21 | 5 | NM_032167.5 | P1 | |
SNX29 | ENST00000564111.5 | n.647C>G | non_coding_transcript_exon_variant | 7/8 | 2 | ||||
SNX29 | ENST00000568359.1 | n.416C>G | non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000269 AC: 41AN: 152154Hom.: 3 Cov.: 31
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GnomAD3 exomes AF: 0.00106 AC: 265AN: 251180Hom.: 4 AF XY: 0.00141 AC XY: 192AN XY: 135742
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GnomAD4 exome AF: 0.000510 AC: 746AN: 1461672Hom.: 14 Cov.: 33 AF XY: 0.000737 AC XY: 536AN XY: 727146
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | SNX29: BP4, BP7, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at