chr4-56966665-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The ENST00000640343.2(REST):c.992C>T(p.Pro331Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000640343.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NOA1 | NM_032313.4 | c.1719G>A | p.Arg573= | synonymous_variant | 5/7 | ENST00000264230.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REST | ENST00000640343.2 | c.992C>T | p.Pro331Leu | missense_variant | 4/4 | 1 | |||
REST | ENST00000640168.2 | c.908C>T | p.Pro303Leu | missense_variant | 3/3 | 1 | |||
NOA1 | ENST00000264230.5 | c.1719G>A | p.Arg573= | synonymous_variant | 5/7 | 1 | NM_032313.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251344Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135868
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1461232Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726982
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | NOA1: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at