7-103989356-TGCCGCCGCCGCCGCC-TGCCGCCGCCGCCGCCGCCGCC
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_005045.4(RELN):c.-6_-1dupGGCGGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,394,188 control chromosomes in the GnomAD database, including 122,293 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.52 ( 20330 hom., cov: 0)
Exomes 𝑓: 0.43 ( 101963 hom. )
Consequence
RELN
NM_005045.4 5_prime_UTR
NM_005045.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.06
Genes affected
RELN (HGNC:9957): (reelin) This gene encodes a large secreted extracellular matrix protein thought to control cell-cell interactions critical for cell positioning and neuronal migration during brain development. This protein may be involved in schizophrenia, autism, bipolar disorder, major depression and in migration defects associated with temporal lobe epilepsy. Mutations of this gene are associated with autosomal recessive lissencephaly with cerebellar hypoplasia. Two transcript variants encoding distinct isoforms have been identified for this gene. Other transcript variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 7-103989356-T-TGCCGCC is Benign according to our data. Variant chr7-103989356-T-TGCCGCC is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 130109.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=5}.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.522 AC: 77298AN: 148096Hom.: 20328 Cov.: 0
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GnomAD3 exomes AF: 0.147 AC: 9416AN: 63892Hom.: 1877 AF XY: 0.156 AC XY: 5772AN XY: 37010
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GnomAD4 exome AF: 0.428 AC: 533190AN: 1245994Hom.: 101963 Cov.: 36 AF XY: 0.429 AC XY: 262976AN XY: 613244
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GnomAD4 genome AF: 0.522 AC: 77336AN: 148194Hom.: 20330 Cov.: 0 AF XY: 0.523 AC XY: 37807AN XY: 72258
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:5
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 01, 2013 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Norman-Roberts syndrome;C4225327:Familial temporal lobe epilepsy 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 03, 2021 | - - |
Lissencephaly, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Norman-Roberts syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Nov 07, 2021 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at