9-104754685-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_015469.3(NIPSNAP3A):c.565G>A(p.Gly189Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,613,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015469.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPSNAP3A | NM_015469.3 | c.565G>A | p.Gly189Arg | missense_variant | 4/6 | ENST00000374767.5 | |
NIPSNAP3A | NM_001329570.2 | c.430+1621G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPSNAP3A | ENST00000374767.5 | c.565G>A | p.Gly189Arg | missense_variant | 4/6 | 1 | NM_015469.3 | P1 | |
NIPSNAP3A | ENST00000471001.1 | n.1087G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251366Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135866
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461422Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727042
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.565G>A (p.G189R) alteration is located in exon 4 (coding exon 4) of the NIPSNAP3A gene. This alteration results from a G to A substitution at nucleotide position 565, causing the glycine (G) at amino acid position 189 to be replaced by an arginine (R). 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