rs736707
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005045.4(RELN):c.9606-57T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,602,426 control chromosomes in the GnomAD database, including 50,574 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 7625 hom., cov: 32)
Exomes 𝑓: 0.23 ( 42949 hom. )
Consequence
RELN
NM_005045.4 intron
NM_005045.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.46
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
Variant 7-103489956-A-G is Benign according to our data. Variant chr7-103489956-A-G is described in ClinVar as [Benign]. Clinvar id is 1295479.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RELN | NM_005045.4 | c.9606-57T>C | intron_variant | ENST00000428762.6 | |||
SLC26A5-AS1 | NR_110141.1 | n.1366-14448A>G | intron_variant, non_coding_transcript_variant | ||||
RELN | NM_173054.3 | c.9606-57T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RELN | ENST00000428762.6 | c.9606-57T>C | intron_variant | 5 | NM_005045.4 | P5 | |||
SLC26A5-AS1 | ENST00000422488.1 | n.1366-14448A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.296 AC: 44880AN: 151858Hom.: 7624 Cov.: 32
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GnomAD4 exome AF: 0.232 AC: 337181AN: 1450450Hom.: 42949 AF XY: 0.236 AC XY: 170094AN XY: 721946
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GnomAD4 genome ? AF: 0.296 AC: 44922AN: 151976Hom.: 7625 Cov.: 32 AF XY: 0.298 AC XY: 22172AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
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