chr14-24408262-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025081.3(NYNRIN):c.592G>A(p.Gly198Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,610,622 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_025081.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NYNRIN | NM_025081.3 | c.592G>A | p.Gly198Ser | missense_variant | 3/9 | ENST00000382554.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NYNRIN | ENST00000382554.4 | c.592G>A | p.Gly198Ser | missense_variant | 3/9 | 5 | NM_025081.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 40AN: 245278Hom.: 0 AF XY: 0.000157 AC XY: 21AN XY: 133444
GnomAD4 exome AF: 0.000117 AC: 170AN: 1458402Hom.: 0 Cov.: 33 AF XY: 0.0000965 AC XY: 70AN XY: 725572
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.592G>A (p.G198S) alteration is located in exon 3 (coding exon 2) of the NYNRIN gene. This alteration results from a G to A substitution at nucleotide position 592, causing the glycine (G) at amino acid position 198 to be replaced by a serine (S). 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