chr1-229442044-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_018230.3(NUP133):c.3335-4A>G 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 0.0000489 in 1,555,122 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_018230.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP133 | NM_018230.3 | c.3335-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000261396.6 | NP_060700.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP133 | ENST00000261396.6 | c.3335-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_018230.3 | ENSP00000261396 | P1 | |||
NUP133 | ENST00000490352.1 | n.382-4A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000289 AC: 44AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000412 AC: 8AN: 193976Hom.: 0 AF XY: 0.0000374 AC XY: 4AN XY: 106856
GnomAD4 exome AF: 0.0000228 AC: 32AN: 1402752Hom.: 1 Cov.: 30 AF XY: 0.0000129 AC XY: 9AN XY: 696752
GnomAD4 genome AF: 0.000289 AC: 44AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.000362 AC XY: 27AN XY: 74518
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at