rs10042
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001197293.3(DPYSL2):c.*2441G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 152,550 control chromosomes in the GnomAD database, including 14 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 0.011 ( 14 hom., cov: 32)
Exomes 𝑓: 0.0092 ( 0 hom. )
Consequence
DPYSL2
NM_001197293.3 3_prime_UTR
NM_001197293.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.262
Genes affected
DPYSL2 (HGNC:3014): (dihydropyrimidinase like 2) This gene encodes a member of the collapsin response mediator protein family. Collapsin response mediator proteins form homo- and hetero-tetramers and facilitate neuron guidance, growth and polarity. The encoded protein promotes microtubule assembly and is required for Sema3A-mediated growth cone collapse, and also plays a role in synaptic signaling through interactions with calcium channels. This gene has been implicated in multiple neurological disorders, and hyperphosphorylation of the encoded protein may play a key role in the development of Alzheimer's disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]
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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=-0.51).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0115 (1748/152116) while in subpopulation NFE AF= 0.0174 (1185/68002). AF 95% confidence interval is 0.0166. There are 14 homozygotes in gnomad4. There are 822 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1748 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPYSL2 | NM_001197293.3 | c.*2441G>A | 3_prime_UTR_variant | 14/14 | ENST00000521913.7 | ||
DPYSL2 | NM_001244604.2 | c.*2441G>A | 3_prime_UTR_variant | 14/14 | |||
DPYSL2 | NM_001386.6 | c.*2441G>A | 3_prime_UTR_variant | 14/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYSL2 | ENST00000521913.7 | c.*2441G>A | 3_prime_UTR_variant | 14/14 | 1 | NM_001197293.3 | |||
DPYSL2 | ENST00000311151.9 | c.*2441G>A | 3_prime_UTR_variant | 14/14 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0115 AC: 1750AN: 151998Hom.: 14 Cov.: 32
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GnomAD4 exome AF: 0.00922 AC: 4AN: 434Hom.: 0 Cov.: 0 AF XY: 0.00769 AC XY: 2AN XY: 260
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GnomAD4 genome ? AF: 0.0115 AC: 1748AN: 152116Hom.: 14 Cov.: 32 AF XY: 0.0111 AC XY: 822AN XY: 74386
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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