rs754048752
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001330078.2(NRXN1):c.2829A>G(p.Leu943=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,427,250 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 (★). Synonymous variant affecting the same amino acid position (i.e. L943L) 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.2829A>G | p.Leu943= | synonymous_variant | 14/23 | ENST00000401669.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN1 | ENST00000401669.7 | c.2829A>G | p.Leu943= | synonymous_variant | 14/23 | 5 | NM_001330078.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000355 AC: 8AN: 225072Hom.: 0 AF XY: 0.0000498 AC XY: 6AN XY: 120600
GnomAD4 exome AF: 0.0000147 AC: 21AN: 1427250Hom.: 0 Cov.: 31 AF XY: 0.0000198 AC XY: 14AN XY: 705518
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Pitt-Hopkins-like syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at