chr7-103472415-C-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_005045.4(RELN):c.*397G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.992 in 256,042 control chromosomes in the GnomAD database, including 126,082 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005045.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RELN | NM_005045.4 | c.*397G>A | 3_prime_UTR_variant | Exon 65 of 65 | ENST00000428762.6 | NP_005036.2 | ||
RELN | NM_173054.3 | c.*397G>A | 3_prime_UTR_variant | Exon 64 of 64 | NP_774959.1 | |||
SLC26A5-AS1 | NR_110141.1 | n.1365+25747C>T | intron_variant | Intron 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.993 AC: 151121AN: 152180Hom.: 75040 Cov.: 33
GnomAD4 exome AF: 0.991 AC: 102850AN: 103744Hom.: 50983 Cov.: 0 AF XY: 0.992 AC XY: 54377AN XY: 54802
GnomAD4 genome AF: 0.993 AC: 151239AN: 152298Hom.: 75099 Cov.: 33 AF XY: 0.993 AC XY: 73953AN XY: 74458
ClinVar
Submissions by phenotype
Norman-Roberts syndrome Benign:1
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:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at