chr2-183158283-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_138285.5(NUP35):c.610A>G(p.Met204Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,554,402 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 Uncertain significance (★).
Frequency
Consequence
NM_138285.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP35 | NM_138285.5 | c.610A>G | p.Met204Val | missense_variant, splice_region_variant | 7/9 | ENST00000295119.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP35 | ENST00000295119.9 | c.610A>G | p.Met204Val | missense_variant, splice_region_variant | 7/9 | 1 | NM_138285.5 | P1 | |
NUP35 | ENST00000409798.5 | c.559A>G | p.Met187Val | missense_variant, splice_region_variant | 8/10 | 2 | |||
NUP35 | ENST00000479162.5 | n.507A>G | splice_region_variant, non_coding_transcript_exon_variant | 6/7 | 2 | ||||
NUP35 | ENST00000374930.7 | c.*9A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000178 AC: 4AN: 225132Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 122178
GnomAD4 exome AF: 0.0000164 AC: 23AN: 1402136Hom.: 0 Cov.: 27 AF XY: 0.0000201 AC XY: 14AN XY: 694918
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.610A>G (p.M204V) alteration is located in exon 7 (coding exon 7) of the NUP35 gene. This alteration results from a A to G substitution at nucleotide position 610, causing the methionine (M) at amino acid position 204 to be replaced by a valine (V). 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