rs144557847
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS1
The NM_005045.4(RELN):c.77C>T(p.Ala26Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000289 in 1,613,098 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. A26A) has been classified as Likely benign.
Frequency
Consequence
NM_005045.4 missense
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.77C>T | p.Ala26Val | missense_variant | 1/65 | ENST00000428762.6 | |
RELN | NM_173054.3 | c.77C>T | p.Ala26Val | missense_variant | 1/64 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RELN | ENST00000428762.6 | c.77C>T | p.Ala26Val | missense_variant | 1/65 | 5 | NM_005045.4 | P5 |
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 218AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000340 AC: 84AN: 246944Hom.: 0 AF XY: 0.000216 AC XY: 29AN XY: 134502
GnomAD4 exome AF: 0.000168 AC: 246AN: 1460880Hom.: 1 Cov.: 32 AF XY: 0.000138 AC XY: 100AN XY: 726772
GnomAD4 genome AF: 0.00145 AC: 220AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.00145 AC XY: 108AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 23, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | RELN: BS1 - |
not specified Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 22, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 31, 2015 | - - |
Norman-Roberts syndrome;C4225327:Familial temporal lobe epilepsy 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
RELN-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 18, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at