rs370521049
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015080.4(NRXN2):c.376C>G(p.Leu126Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000027 in 1,371,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L126M) has been classified as Uncertain significance.
Frequency
Consequence
NM_015080.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN2 | NM_015080.4 | c.376C>G | p.Leu126Val | missense_variant | 2/23 | ENST00000265459.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN2 | ENST00000265459.11 | c.376C>G | p.Leu126Val | missense_variant | 2/23 | 5 | NM_015080.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000527 AC: 8AN: 151662Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000238 AC: 29AN: 1219330Hom.: 0 Cov.: 34 AF XY: 0.0000235 AC XY: 14AN XY: 595274
GnomAD4 genome ? AF: 0.0000527 AC: 8AN: 151770Hom.: 0 Cov.: 34 AF XY: 0.0000943 AC XY: 7AN XY: 74196
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.376C>G (p.L126V) alteration is located in exon 2 (coding exon 1) of the NRXN2 gene. This alteration results from a C to G substitution at nucleotide position 376, causing the leucine (L) at amino acid position 126 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at