14-24407864-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_025081.3(NYNRIN):c.199-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000935 in 1,594,338 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_025081.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NYNRIN | NM_025081.3 | c.199-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000382554.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NYNRIN | ENST00000382554.4 | c.199-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_025081.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000140 AC: 33AN: 235418Hom.: 0 AF XY: 0.000133 AC XY: 17AN XY: 127650
GnomAD4 exome AF: 0.0000506 AC: 73AN: 1442014Hom.: 0 Cov.: 32 AF XY: 0.0000517 AC XY: 37AN XY: 715402
GnomAD4 genome AF: 0.000499 AC: 76AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at