NM_015080.4:c.4519C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015080.4(NRXN2):c.4519C>T(p.Pro1507Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000606 in 1,601,796 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 Uncertain significance (★★).
Frequency
Consequence
NM_015080.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRXN2 | ENST00000265459.11 | c.4519C>T | p.Pro1507Ser | missense_variant | Exon 23 of 23 | 5 | NM_015080.4 | ENSP00000265459.5 | ||
NRXN2 | ENST00000704782.1 | c.4528C>T | p.Pro1510Ser | missense_variant | Exon 22 of 22 | ENSP00000516031.1 | ||||
NRXN2 | ENST00000704781.1 | c.4262-316C>T | intron_variant | Intron 21 of 21 | ENSP00000516029.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152086Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000498 AC: 11AN: 220924Hom.: 0 AF XY: 0.0000417 AC XY: 5AN XY: 120038
GnomAD4 exome AF: 0.0000642 AC: 93AN: 1449710Hom.: 0 Cov.: 34 AF XY: 0.0000583 AC XY: 42AN XY: 719884
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152086Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:2
The c.4519C>T (p.P1507S) alteration is located in exon 23 (coding exon 22) of the NRXN2 gene. This alteration results from a C to T substitution at nucleotide position 4519, causing the proline (P) at amino acid position 1507 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at