chr14-24408323-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025081.3(NYNRIN):c.653C>T(p.Pro218Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NYNRIN | NM_025081.3 | c.653C>T | p.Pro218Leu | missense_variant | 3/9 | ENST00000382554.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NYNRIN | ENST00000382554.4 | c.653C>T | p.Pro218Leu | missense_variant | 3/9 | 5 | NM_025081.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248192Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134834
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461312Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 726942
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152336Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74492
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at