2-219250304-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006000.3(TUBA4A):c.*48G>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 0.0109 in 1,552,174 control chromosomes in the GnomAD database, including 382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 52 hom., cov: 32)
Exomes 𝑓: 0.011 ( 330 hom. )
Consequence
TUBA4A
NM_006000.3 3_prime_UTR
NM_006000.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.930
Genes affected
STK16 (HGNC:11394): (serine/threonine kinase 16) Predicted to enable protein serine/threonine kinase activity. Involved in protein autophosphorylation. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
TUBA4A (HGNC:12407): (tubulin alpha 4a) Microtubules of the eukaryotic cytoskeleton perform essential and diverse functions and are composed of a heterodimer of alpha and beta tubulin. The genes encoding these microtubule constituents are part of the tubulin superfamily, which is composed of six distinct families. Genes from the alpha, beta and gamma tubulin families are found in all eukaryotes. The alpha and beta tubulins represent the major components of microtubules, while gamma tubulin plays a critical role in the nucleation of microtubule assembly. There are multiple alpha and beta tubulin genes and they are highly conserved among and between species. This gene encodes an alpha tubulin that is a highly conserved homolog of a rat testis-specific alpha tubulin. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 2-219250304-C-T is Benign according to our data. Variant chr2-219250304-C-T is described in ClinVar as [Benign]. Clinvar id is 1227287.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STK16 | NM_001330213.2 | c.*1745C>T | 3_prime_UTR_variant | 8/8 | ENST00000396738.7 | ||
TUBA4A | NM_006000.3 | c.*48G>A | 3_prime_UTR_variant | 4/4 | ENST00000248437.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBA4A | ENST00000248437.9 | c.*48G>A | 3_prime_UTR_variant | 4/4 | 1 | NM_006000.3 | P1 | ||
STK16 | ENST00000396738.7 | c.*1745C>T | 3_prime_UTR_variant | 8/8 | 2 | NM_001330213.2 | P1 | ||
STK16 | ENST00000409638.7 | c.*1745C>T | 3_prime_UTR_variant | 8/8 | 1 | P1 | |||
TUBA4A | ENST00000392088.6 | c.*48G>A | 3_prime_UTR_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0128 AC: 1942AN: 152224Hom.: 47 Cov.: 32
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GnomAD3 exomes AF: 0.0209 AC: 4306AN: 205982Hom.: 234 AF XY: 0.0173 AC XY: 1906AN XY: 110010
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GnomAD4 exome AF: 0.0107 AC: 15042AN: 1399832Hom.: 330 Cov.: 31 AF XY: 0.0102 AC XY: 7059AN XY: 689624
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GnomAD4 genome ? AF: 0.0128 AC: 1953AN: 152342Hom.: 52 Cov.: 32 AF XY: 0.0129 AC XY: 958AN XY: 74488
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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 | GeneDx | Sep 18, 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