rs1063178
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_007240.3(DUSP12):c.510C>T(p.Tyr170=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 1,609,770 control chromosomes in the GnomAD database, including 93,685 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 0.35 ( 9292 hom., cov: 32)
Exomes 𝑓: 0.34 ( 84393 hom. )
Consequence
DUSP12
NM_007240.3 synonymous
NM_007240.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.575
Genes affected
DUSP12 (HGNC:3067): (dual specificity phosphatase 12) The protein encoded by this gene is a member of the dual specificity protein phosphatase subfamily. These phosphatases inactivate their target kinases by dephosphorylating both the phosphoserine/threonine and phosphotyrosine residues. They negatively regulate members of the mitogen-activated protein (MAP) kinase superfamily (MAPK/ERK, SAPK/JNK, p38), which is associated with cellular proliferation and differentiation. Different members of the family of dual specificity phosphatases show distinct substrate specificities for various MAP kinases, different tissue distribution and subcellular localization, and different modes of inducibility of their expression by extracellular stimuli. This gene product is the human ortholog of the Saccharomyces cerevisiae YVH1 protein tyrosine phosphatase. It is localized predominantly in the nucleus, and is novel in that it contains, and is regulated by a zinc finger domain. [provided by RefSeq, Jul 2008]
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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=-0.52).
BP7
?
Synonymous conserved (PhyloP=0.575 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DUSP12 | NM_007240.3 | c.510C>T | p.Tyr170= | synonymous_variant | 3/6 | ENST00000367943.5 | |
DUSP12 | XM_005244862.4 | c.120C>T | p.Tyr40= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DUSP12 | ENST00000367943.5 | c.510C>T | p.Tyr170= | synonymous_variant | 3/6 | 1 | NM_007240.3 | P1 | |
ATF6-DT | ENST00000702792.1 | n.373-1550G>A | intron_variant, non_coding_transcript_variant | ||||||
DUSP12 | ENST00000464004.2 | c.*109C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/5 | 2 | ||||
DUSP12 | ENST00000484291.5 | c.*57+136C>T | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.347 AC: 52696AN: 151800Hom.: 9287 Cov.: 32
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GnomAD3 exomes AF: 0.335 AC: 84034AN: 250490Hom.: 14682 AF XY: 0.338 AC XY: 45739AN XY: 135410
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GnomAD4 exome AF: 0.337 AC: 490801AN: 1457852Hom.: 84393 Cov.: 35 AF XY: 0.338 AC XY: 244874AN XY: 725348
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GnomAD4 genome ? AF: 0.347 AC: 52724AN: 151918Hom.: 9292 Cov.: 32 AF XY: 0.347 AC XY: 25751AN XY: 74228
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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