chr2-183130414-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138285.5(NUP35):c.212-4G>A 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 0.0000469 in 1,322,638 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_138285.5 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
NUP35 | NM_138285.5 | c.212-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000295119.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP35 | ENST00000295119.9 | c.212-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_138285.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000677 AC: 7AN: 103350Hom.: 0 Cov.: 25
GnomAD3 exomes AF: 0.0000812 AC: 18AN: 221758Hom.: 0 AF XY: 0.0000663 AC XY: 8AN XY: 120696
GnomAD4 exome AF: 0.0000451 AC: 55AN: 1219272Hom.: 0 Cov.: 32 AF XY: 0.0000343 AC XY: 21AN XY: 612468
GnomAD4 genome AF: 0.0000677 AC: 7AN: 103366Hom.: 0 Cov.: 25 AF XY: 0.0000835 AC XY: 4AN XY: 47916
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at