chr5-147408788-G-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001197294.2(DPYSL3):āc.972C>Gā(p.Thr324=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00228 in 1,614,130 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.012 ( 43 hom., cov: 32)
Exomes š: 0.0013 ( 39 hom. )
Consequence
DPYSL3
NM_001197294.2 synonymous
NM_001197294.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.870
Genes affected
DPYSL3 (HGNC:3015): (dihydropyrimidinase like 3) Enables filamin binding activity. Predicted to be involved in several processes, including actin filament organization; regulation of plasma membrane bounded cell projection organization; and response to axon injury. Predicted to act upstream of or within nervous system development. Predicted to be located in several cellular components, including cell body; growth cone; and lamellipodium. Predicted to be part of filamentous actin. Predicted to be active in synapse. Predicted to colocalize with exocytic vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 5-147408788-G-C is Benign according to our data. Variant chr5-147408788-G-C is described in ClinVar as [Benign]. Clinvar id is 786065.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.87 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.012 (1834/152258) while in subpopulation AFR AF= 0.0423 (1758/41538). AF 95% confidence interval is 0.0407. There are 43 homozygotes in gnomad4. There are 884 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 43 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPYSL3 | NM_001197294.2 | c.972C>G | p.Thr324= | synonymous_variant | 7/14 | ENST00000343218.10 | |
DPYSL3 | NM_001387.3 | c.630C>G | p.Thr210= | synonymous_variant | 7/14 | ||
DPYSL3 | XM_011537574.3 | c.618C>G | p.Thr206= | synonymous_variant | 7/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYSL3 | ENST00000343218.10 | c.972C>G | p.Thr324= | synonymous_variant | 7/14 | 1 | NM_001197294.2 | ||
DPYSL3 | ENST00000398514.7 | c.630C>G | p.Thr210= | synonymous_variant | 7/14 | 1 | P1 | ||
DPYSL3 | ENST00000519672.1 | n.512C>G | non_coding_transcript_exon_variant | 6/6 | 3 | ||||
DPYSL3 | ENST00000507309.5 | n.96-9536C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0120 AC: 1826AN: 152142Hom.: 42 Cov.: 32
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GnomAD3 exomes AF: 0.00303 AC: 755AN: 249514Hom.: 13 AF XY: 0.00228 AC XY: 308AN XY: 135370
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GnomAD4 exome AF: 0.00126 AC: 1843AN: 1461872Hom.: 39 Cov.: 30 AF XY: 0.00107 AC XY: 775AN XY: 727240
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GnomAD4 genome AF: 0.0120 AC: 1834AN: 152258Hom.: 43 Cov.: 32 AF XY: 0.0119 AC XY: 884AN XY: 74438
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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 | Invitae | Jul 23, 2018 | - - |
Computational 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