rs618923
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000227322.8(ZPR1):c.981+87T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,191,872 control chromosomes in the GnomAD database, including 31,695 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 0.19 ( 3358 hom., cov: 32)
Exomes 𝑓: 0.22 ( 28337 hom. )
Consequence
ZPR1
ENST00000227322.8 intron
ENST00000227322.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.633
Genes affected
ZPR1 (HGNC:13051): (ZPR1 zinc finger) The protein encoded by this gene is found in the cytoplasm of quiescent cells but translocates to the nucleolus in proliferating cells. The encoded protein interacts with survival motor neuron protein (SMN1) to enhance pre-mRNA splicing and to induce neuronal differentiation and axonal growth. Defects in this gene or the SMN1 gene can cause spinal muscular atrophy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZPR1 | NM_003904.5 | c.981+87T>C | intron_variant | ENST00000227322.8 | NP_003895.1 | |||
ZPR1 | NM_001317086.2 | c.819+87T>C | intron_variant | NP_001304015.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZPR1 | ENST00000227322.8 | c.981+87T>C | intron_variant | 1 | NM_003904.5 | ENSP00000227322 | P1 | |||
ZPR1 | ENST00000429220.5 | c.760+87T>C | intron_variant | 5 | ENSP00000394495 | |||||
ZPR1 | ENST00000444935.5 | c.980+87T>C | intron_variant | 5 | ENSP00000390391 | |||||
ZPR1 | ENST00000449430.1 | c.*184+87T>C | intron_variant, NMD_transcript_variant | 3 | ENSP00000415505 |
Frequencies
GnomAD3 genomes AF: 0.195 AC: 29600AN: 151976Hom.: 3352 Cov.: 32
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GnomAD4 exome AF: 0.224 AC: 232781AN: 1039778Hom.: 28337 AF XY: 0.224 AC XY: 119314AN XY: 532980
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GnomAD4 genome AF: 0.195 AC: 29628AN: 152094Hom.: 3358 Cov.: 32 AF XY: 0.192 AC XY: 14281AN XY: 74360
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at