8-11331493-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_054028.2(SLC35G5):c.387C>T(p.Asn129Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000291 in 1,613,948 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 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 2 hom. )
Consequence
SLC35G5
NM_054028.2 synonymous
NM_054028.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.234
Genes affected
SLC35G5 (HGNC:15546): (solute carrier family 35 member G5) This gene is intronless and probably arose from retrotransposition of a similar gene. It has high sequence similarity to the gene encoding acyl-malonyl condensing enzyme on chromosome 17. [provided by RefSeq, Aug 2011]
MTMR9 (HGNC:14596): (myotubularin related protein 9) This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. [provided by RefSeq, Jul 2008]
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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=-0.52).
BP6
Variant 8-11331493-C-T is Benign according to our data. Variant chr8-11331493-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658402.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.234 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000545 AC: 137AN: 251166Hom.: 2 AF XY: 0.000611 AC XY: 83AN XY: 135738
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GnomAD4 exome AF: 0.000291 AC: 425AN: 1461672Hom.: 2 Cov.: 154 AF XY: 0.000311 AC XY: 226AN XY: 727146
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GnomAD4 genome AF: 0.000289 AC: 44AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74452
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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
Nov 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SLC35G5: BP4, BP7 -
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at