1-231694105-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018662.3(DISC1):c.347C>T(p.Ala116Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,614,166 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018662.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DISC1 | NM_018662.3 | c.347C>T | p.Ala116Val | missense_variant | 2/13 | ENST00000439617.8 | |
TSNAX-DISC1 | NR_028393.1 | n.1068C>T | non_coding_transcript_exon_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DISC1 | ENST00000439617.8 | c.347C>T | p.Ala116Val | missense_variant | 2/13 | 5 | NM_018662.3 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00100 AC: 249AN: 248896Hom.: 3 AF XY: 0.000861 AC XY: 116AN XY: 134762
GnomAD4 exome AF: 0.000270 AC: 394AN: 1461870Hom.: 4 Cov.: 32 AF XY: 0.000263 AC XY: 191AN XY: 727236
GnomAD4 genome AF: 0.000486 AC: 74AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000564 AC XY: 42AN XY: 74482
ClinVar
Submissions by phenotype
DISC1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2019 | This variant is classified as 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