chr1-154001017-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The ENST00000368559.8(NUP210L):c.5225A>G(p.His1742Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H1742N) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000368559.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NUP210L | NM_207308.3 | c.5225A>G | p.His1742Arg | missense_variant | 37/40 | ENST00000368559.8 | |
NUP210L | XM_011510122.2 | c.5093A>G | p.His1698Arg | missense_variant | 36/39 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.5225A>G | p.His1742Arg | missense_variant | 37/40 | 5 | NM_207308.3 | P2 | |
NUP210L | ENST00000368553.5 | c.1730-5837A>G | intron_variant | 1 | A2 | ||||
NUP210L | ENST00000271854.3 | c.4931-5837A>G | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151878Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249536Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135382
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461870Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151996Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at