rs373654735
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001330078.2(NRXN1):c.864A>T(p.Gly288=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G288G) has been classified as Likely benign.
Frequency
Consequence
NM_001330078.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN1 | NM_001330078.2 | c.864A>T | p.Gly288= | synonymous_variant | 6/23 | ENST00000401669.7 | |
LOC101927089 | XR_245002.5 | n.89-1227T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN1 | ENST00000401669.7 | c.864A>T | p.Gly288= | synonymous_variant | 6/23 | 5 | NM_001330078.2 | A1 | |
ENST00000634985.1 | n.50-1227T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248082Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134566
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460370Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726366
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at