rs2072403
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005045.4(RELN):c.1776A>G(p.Glu592Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0593 in 1,610,778 control chromosomes in the GnomAD database, including 3,875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005045.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0939 AC: 14227AN: 151542Hom.: 944 Cov.: 32
GnomAD3 exomes AF: 0.0752 AC: 18762AN: 249660Hom.: 978 AF XY: 0.0691 AC XY: 9330AN XY: 134978
GnomAD4 exome AF: 0.0557 AC: 81210AN: 1459118Hom.: 2924 Cov.: 31 AF XY: 0.0545 AC XY: 39591AN XY: 725888
GnomAD4 genome AF: 0.0941 AC: 14264AN: 151660Hom.: 951 Cov.: 32 AF XY: 0.0945 AC XY: 7001AN XY: 74104
ClinVar
Submissions by phenotype
not specified Benign:3
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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Norman-Roberts syndrome Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:2
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Norman-Roberts syndrome;C4225327:Familial temporal lobe epilepsy 7 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at