8-35235796-G-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_080872.4(UNC5D):c.12G>T(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,229,838 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0072 ( 10 hom., cov: 33)
Exomes 𝑓: 0.011 ( 68 hom. )
Consequence
UNC5D
NM_080872.4 synonymous
NM_080872.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.14
Genes affected
UNC5D (HGNC:18634): (unc-5 netrin receptor D) Predicted to enable netrin receptor activity. Involved in cell-cell adhesion via plasma-membrane adhesion molecules. Predicted to be located in cell surface and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.39).
BP6
Variant 8-35235796-G-T is Benign according to our data. Variant chr8-35235796-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 778358.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BS2
High AC in GnomAd4 at 1100 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5D | NM_080872.4 | c.12G>T | p.Ala4= | synonymous_variant | 1/17 | ENST00000404895.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5D | ENST00000404895.7 | c.12G>T | p.Ala4= | synonymous_variant | 1/17 | 1 | NM_080872.4 | P4 | |
UNC5D | ENST00000416672.5 | c.12G>T | p.Ala4= | synonymous_variant | 1/18 | 5 | A1 | ||
UNC5D | ENST00000420357.5 | c.12G>T | p.Ala4= | synonymous_variant | 1/15 | 5 | |||
UNC5D | ENST00000287272.6 | c.12G>T | p.Ala4= | synonymous_variant | 1/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00723 AC: 1099AN: 152092Hom.: 10 Cov.: 33
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GnomAD3 exomes AF: 0.00862 AC: 6AN: 696Hom.: 0 AF XY: 0.00220 AC XY: 1AN XY: 454
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GnomAD4 exome AF: 0.0107 AC: 11487AN: 1077638Hom.: 68 Cov.: 30 AF XY: 0.0105 AC XY: 5364AN XY: 508938
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GnomAD4 genome AF: 0.00723 AC: 1100AN: 152200Hom.: 10 Cov.: 33 AF XY: 0.00735 AC XY: 547AN XY: 74396
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at