rs1345247825
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_005045.4(RELN):c.8121G>C(p.Val2707Val) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V2707V) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
RELN
NM_005045.4 splice_region, synonymous
NM_005045.4 splice_region, synonymous
Scores
2
Splicing: ADA: 0.002875
2
Clinical Significance
Conservation
PhyloP100: 1.36
Publications
0 publications found
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 was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 7-103511004-C-G is Benign according to our data. Variant chr7-103511004-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2934348.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.36 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005045.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RELN | NM_005045.4 | MANE Select | c.8121G>C | p.Val2707Val | splice_region synonymous | Exon 51 of 65 | NP_005036.2 | ||
| RELN | NM_173054.3 | c.8121G>C | p.Val2707Val | splice_region synonymous | Exon 51 of 64 | NP_774959.1 | |||
| SLC26A5-AS1 | NR_110141.1 | n.1487-1765C>G | intron | N/A |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RELN | ENST00000428762.6 | TSL:5 MANE Select | c.8121G>C | p.Val2707Val | splice_region synonymous | Exon 51 of 65 | ENSP00000392423.1 | ||
| SLC26A5-AS1 | ENST00000422488.1 | TSL:1 | n.1487-1765C>G | intron | N/A | ||||
| RELN | ENST00000424685.3 | TSL:5 | c.8121G>C | p.Val2707Val | splice_region synonymous | Exon 51 of 65 | ENSP00000388446.3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250840 AF XY: 0.00000738 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
250840
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460732Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726710 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1460732
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
726710
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33446
American (AMR)
AF:
AC:
0
AN:
44656
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26114
East Asian (EAS)
AF:
AC:
0
AN:
39668
South Asian (SAS)
AF:
AC:
0
AN:
86188
European-Finnish (FIN)
AF:
AC:
0
AN:
53414
Middle Eastern (MID)
AF:
AC:
0
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1111124
Other (OTH)
AF:
AC:
0
AN:
60358
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
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Allele balance
Age Distribution
Exome Het
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Norman-Roberts syndrome;C4225327:Familial temporal lobe epilepsy 7 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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