1-154142229-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_207308.3(NUP210L):c.473-705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 150,822 control chromosomes in the GnomAD database, including 7,860 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.30 ( 7860 hom., cov: 30)
Consequence
NUP210L
NM_207308.3 intron
NM_207308.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.08
Genes affected
NUP210L (HGNC:29915): (nucleoporin 210 like) Predicted to act upstream of or within Sertoli cell development and spermatid development. Predicted to be integral component of membrane. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NUP210L | NM_207308.3 | c.473-705G>A | intron_variant | NP_997191.2 | ||||
NUP210L | NM_001159484.1 | c.473-705G>A | intron_variant | NP_001152956.1 | ||||
NUP210L | XM_017002788.3 | c.473-705G>A | intron_variant | XP_016858277.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NUP210L | ENST00000368559.8 | c.473-705G>A | intron_variant | 5 | ENSP00000357547.3 | |||||
NUP210L | ENST00000271854.3 | c.473-705G>A | intron_variant | 5 | ENSP00000271854.3 |
Frequencies
GnomAD3 genomes AF: 0.304 AC: 45789AN: 150728Hom.: 7855 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.304 AC: 45810AN: 150822Hom.: 7860 Cov.: 30 AF XY: 0.311 AC XY: 22857AN XY: 73562
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at