5-168710971-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_003062.4(SLIT3):c.2643C>T(p.Ile881Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000249 in 1,566,942 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 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
SLIT3
NM_003062.4 synonymous
NM_003062.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.587
Genes affected
SLIT3 (HGNC:11087): (slit guidance ligand 3) The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
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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 5-168710971-G-A is Benign according to our data. Variant chr5-168710971-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2498992.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.587 with no splicing effect.
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLIT3 | NM_003062.4 | c.2643C>T | p.Ile881Ile | synonymous_variant | Exon 25 of 36 | ENST00000519560.6 | NP_003053.2 | |
SLIT3 | NM_001271946.2 | c.2643C>T | p.Ile881Ile | synonymous_variant | Exon 25 of 36 | NP_001258875.2 | ||
SLIT3 | XM_017009779.1 | c.2454C>T | p.Ile818Ile | synonymous_variant | Exon 25 of 36 | XP_016865268.1 | ||
SLIT3-AS2 | NR_130737.1 | n.698+771G>A | intron_variant | Intron 3 of 6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLIT3 | ENST00000519560.6 | c.2643C>T | p.Ile881Ile | synonymous_variant | Exon 25 of 36 | 1 | NM_003062.4 | ENSP00000430333.2 | ||
SLIT3 | ENST00000332966.8 | c.2643C>T | p.Ile881Ile | synonymous_variant | Exon 25 of 36 | 1 | ENSP00000332164.8 | |||
SLIT3-AS2 | ENST00000522615.1 | n.2227+771G>A | intron_variant | Intron 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000285 AC: 5AN: 175632Hom.: 0 AF XY: 0.0000430 AC XY: 4AN XY: 92998
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GnomAD4 exome AF: 0.0000219 AC: 31AN: 1414760Hom.: 0 Cov.: 32 AF XY: 0.0000272 AC XY: 19AN XY: 699016
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74326
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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
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SLIT3: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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