rs139102992
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS1
The NM_005045.4(RELN):c.5274G>T(p.Ala1758=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000285 in 1,611,966 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A1758A) has been classified as Likely benign.
Frequency
Consequence
NM_005045.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RELN | NM_005045.4 | c.5274G>T | p.Ala1758= | synonymous_variant | 35/65 | ENST00000428762.6 | |
RELN | NM_173054.3 | c.5274G>T | p.Ala1758= | synonymous_variant | 35/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RELN | ENST00000428762.6 | c.5274G>T | p.Ala1758= | synonymous_variant | 35/65 | 5 | NM_005045.4 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000186 AC: 28AN: 150514Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251170Hom.: 1 AF XY: 0.000169 AC XY: 23AN XY: 135750
GnomAD4 exome AF: 0.000295 AC: 431AN: 1461452Hom.: 1 Cov.: 34 AF XY: 0.000274 AC XY: 199AN XY: 727022
GnomAD4 genome ? AF: 0.000186 AC: 28AN: 150514Hom.: 0 Cov.: 30 AF XY: 0.000177 AC XY: 13AN XY: 73294
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | RELN: BP4, BP7 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 27, 2014 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Norman-Roberts syndrome;C4225327:Familial temporal lobe epilepsy 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at