chr2-73831039-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_213622.4(STAMBP):c.183C>T(p.Ile61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,614,028 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000094 ( 2 hom. )
Consequence
STAMBP
NM_213622.4 synonymous
NM_213622.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.226
Genes affected
STAMBP (HGNC:16950): (STAM binding protein) Cytokine-mediated signal transduction in the JAK-STAT cascade requires the involvement of adaptor molecules. One such signal-transducing adaptor molecule contains an SH3 domain that is required for induction of MYC and cell growth. The protein encoded by this gene binds to the SH3 domain of the signal-transducing adaptor molecule, and plays a critical role in cytokine-mediated signaling for MYC induction and cell cycle progression. Multiple alternatively spliced transcript variants encoding the same protein isoform have been found for this gene. [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=-0.35).
BP6
Variant 2-73831039-C-T is Benign according to our data. Variant chr2-73831039-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 711304.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.226 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0000937 (137/1461796) while in subpopulation AMR AF= 0.00038 (17/44724). AF 95% confidence interval is 0.000242. There are 2 homozygotes in gnomad4_exome. There are 73 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAMBP | NM_213622.4 | c.183C>T | p.Ile61= | synonymous_variant | 2/10 | ENST00000394070.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAMBP | ENST00000394070.7 | c.183C>T | p.Ile61= | synonymous_variant | 2/10 | 1 | NM_213622.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152232Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000183 AC: 46AN: 251476Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135914
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GnomAD4 exome AF: 0.0000937 AC: 137AN: 1461796Hom.: 2 Cov.: 31 AF XY: 0.000100 AC XY: 73AN XY: 727214
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GnomAD4 genome AF: 0.000118 AC: 18AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74386
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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