chr5-74767425-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014886.6(NSA2):c.3+62T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,598,790 control chromosomes in the GnomAD database, including 12,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1498 hom., cov: 32)
Exomes 𝑓: 0.12 ( 11379 hom. )
Consequence
NSA2
NM_014886.6 intron
NM_014886.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.714
Genes affected
NSA2 (HGNC:30728): (NSA2 ribosome biogenesis factor) This gene encodes a nucleolar protein involved in cell cycle regulation and proliferation. This gene was identified based on sequence similarity to a highly conserved Saccharomyces cerevisiae gene encoding a pre-ribosomal protein, which is involved in large ribosomal subunit biogenesis. The encoded protein is found at elevated levels in diabetic nephropathy. Alternative splicing results in multiple transcript variants. Several related pseudogenes have been identified. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 5-74767425-T-C is Benign according to our data. Variant chr5-74767425-T-C is described in ClinVar as [Benign]. Clinvar id is 1234496.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSA2 | NM_014886.6 | c.3+62T>C | intron_variant | ENST00000610426.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSA2 | ENST00000610426.5 | c.3+62T>C | intron_variant | 1 | NM_014886.6 | P1 | |||
NSA2 | ENST00000296802.9 | c.3+62T>C | intron_variant | 5 | |||||
NSA2 | ENST00000513356.1 | n.101+62T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
NSA2 | ENST00000514918.5 | n.116+62T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20420AN: 152028Hom.: 1498 Cov.: 32
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GnomAD4 exome AF: 0.121 AC: 175571AN: 1446644Hom.: 11379 AF XY: 0.121 AC XY: 87358AN XY: 719332
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GnomAD4 genome AF: 0.134 AC: 20425AN: 152146Hom.: 1498 Cov.: 32 AF XY: 0.134 AC XY: 9945AN XY: 74412
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at