chr2-183159573-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PM2BP4_Strong
The NM_138285.5(NUP35):c.824C>T(p.Thr275Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138285.5 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 |
---|---|---|---|---|---|---|---|
NUP35 | NM_138285.5 | c.824C>T | p.Thr275Ile | missense_variant | 8/9 | ENST00000295119.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP35 | ENST00000295119.9 | c.824C>T | p.Thr275Ile | missense_variant | 8/9 | 1 | NM_138285.5 | P1 | |
NUP35 | ENST00000409798.5 | c.773C>T | p.Thr258Ile | missense_variant | 9/10 | 2 | |||
NUP35 | ENST00000479162.5 | n.721C>T | non_coding_transcript_exon_variant | 7/7 | 2 | ||||
NUP35 | ENST00000374930.7 | c.*223C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251262Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135806
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461156Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 726902
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2022 | The c.824C>T (p.T275I) alteration is located in exon 8 (coding exon 8) of the NUP35 gene. This alteration results from a C to T substitution at nucleotide position 824, causing the threonine (T) at amino acid position 275 to be replaced by an isoleucine (I). 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