11-64648294-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015080.4(NRXN2):c.3328G>A(p.Val1110Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,108 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict 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 -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NRXN2 | ENST00000265459.11 | c.3328G>A | p.Val1110Ile | missense_variant | Exon 17 of 23 | 5 | NM_015080.4 | ENSP00000265459.5 | ||
NRXN2 | ENST00000704782.1 | c.3337G>A | p.Val1113Ile | missense_variant | Exon 16 of 22 | ENSP00000516031.1 | ||||
NRXN2 | ENST00000704781.1 | c.3337G>A | p.Val1113Ile | missense_variant | Exon 16 of 22 | ENSP00000516029.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251394Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135882
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727242
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3328G>A (p.V1110I) alteration is located in exon 17 (coding exon 16) of the NRXN2 gene. This alteration results from a G to A substitution at nucleotide position 3328, causing the valine (V) at amino acid position 1110 to be replaced by an isoleucine (I). 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