rs181686738
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015080.4(NRXN2):āc.1580A>Gā(p.Asn527Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,614,054 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015080.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN2 | NM_015080.4 | c.1580A>G | p.Asn527Ser | missense_variant | 9/23 | ENST00000265459.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN2 | ENST00000265459.11 | c.1580A>G | p.Asn527Ser | missense_variant | 9/23 | 5 | NM_015080.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000419 AC: 105AN: 250806Hom.: 0 AF XY: 0.000582 AC XY: 79AN XY: 135650
GnomAD4 exome AF: 0.000191 AC: 279AN: 1461756Hom.: 4 Cov.: 32 AF XY: 0.000296 AC XY: 215AN XY: 727194
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 11, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at