chr17-59890847-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_016261.4(TUBD1):c.156T>C(p.Ser52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,612,772 control chromosomes in the GnomAD database, including 272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 128 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 144 hom. )
Consequence
TUBD1
NM_016261.4 synonymous
NM_016261.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0480
Genes affected
TUBD1 (HGNC:16811): (tubulin delta 1) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and positive regulation of smoothened signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
?
Variant 17-59890847-A-G is Benign according to our data. Variant chr17-59890847-A-G is described in ClinVar as [Benign]. Clinvar id is 778719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.048 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0758 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBD1 | NM_016261.4 | c.156T>C | p.Ser52= | synonymous_variant | 2/9 | ENST00000325752.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBD1 | ENST00000325752.8 | c.156T>C | p.Ser52= | synonymous_variant | 2/9 | 5 | NM_016261.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0225 AC: 3427AN: 152142Hom.: 125 Cov.: 32
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GnomAD3 exomes AF: 0.00615 AC: 1535AN: 249540Hom.: 47 AF XY: 0.00443 AC XY: 598AN XY: 134936
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GnomAD4 exome AF: 0.00254 AC: 3711AN: 1460512Hom.: 144 Cov.: 31 AF XY: 0.00222 AC XY: 1611AN XY: 726550
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GnomAD4 genome ? AF: 0.0227 AC: 3456AN: 152260Hom.: 128 Cov.: 32 AF XY: 0.0216 AC XY: 1605AN XY: 74454
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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 05, 2018 | - - |
Computational 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at