chr11-117203888-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003186.5(TAGLN):c.461+4T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00322 in 1,613,086 control chromosomes in the GnomAD database, including 148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.017 ( 76 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 72 hom. )
Consequence
TAGLN
NM_003186.5 splice_donor_region, intron
NM_003186.5 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00005573
2
Clinical Significance
Conservation
PhyloP100: -1.61
Genes affected
TAGLN (HGNC:11553): (transgelin) This gene encodes a shape change and transformation sensitive actin-binding protein which belongs to the calponin family. It is ubiquitously expressed in vascular and visceral smooth muscle, and is an early marker of smooth muscle differentiation. The encoded protein is thought to be involved in calcium-independent smooth muscle contraction. It acts as a tumor suppressor, and the loss of its expression is an early event in cell transformation and the development of some tumors, coinciding with cellular plasticity. The encoded protein has a domain architecture consisting of an N-terminal calponin homology (CH) domain and a C-terminal calponin-like (CLIK) domain. Mice with a knockout of the orthologous gene are viable and fertile but their vascular smooth muscle cells exhibit alterations in the distribution of the actin filament and changes in cytoskeletal organization. [provided by RefSeq, Aug 2017]
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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=-0.76).
BP6
?
Variant 11-117203888-T-C is Benign according to our data. Variant chr11-117203888-T-C is described in ClinVar as [Benign]. Clinvar id is 779318.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAGLN | NM_003186.5 | c.461+4T>C | splice_donor_region_variant, intron_variant | ENST00000392951.9 | |||
TAGLN | NM_001001522.2 | c.461+4T>C | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAGLN | ENST00000392951.9 | c.461+4T>C | splice_donor_region_variant, intron_variant | 1 | NM_003186.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0175 AC: 2658AN: 152140Hom.: 76 Cov.: 32
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GnomAD3 exomes AF: 0.00459 AC: 1153AN: 251174Hom.: 36 AF XY: 0.00356 AC XY: 483AN XY: 135754
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GnomAD4 exome AF: 0.00173 AC: 2532AN: 1460828Hom.: 72 Cov.: 30 AF XY: 0.00152 AC XY: 1105AN XY: 726792
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GnomAD4 genome ? AF: 0.0175 AC: 2661AN: 152258Hom.: 76 Cov.: 32 AF XY: 0.0171 AC XY: 1275AN XY: 74450
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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 | Jun 27, 2018 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at