rs201485014
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001330078.2(NRXN1):āc.1326A>Gā(p.Val442=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000895 in 1,453,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. V442V) has been classified as Likely benign.
Frequency
Consequence
NM_001330078.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN1 | NM_001330078.2 | c.1326A>G | p.Val442= | synonymous_variant | 9/23 | ENST00000401669.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN1 | ENST00000401669.7 | c.1326A>G | p.Val442= | synonymous_variant | 9/23 | 5 | NM_001330078.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243002Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132076
GnomAD4 exome AF: 0.00000895 AC: 13AN: 1453296Hom.: 0 Cov.: 31 AF XY: 0.00000969 AC XY: 7AN XY: 722634
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pitt-Hopkins-like syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at