15-81002887-C-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_022566.3(TLNRD1):c.616C>A(p.Arg206=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,597,234 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 1 hom. )
Consequence
TLNRD1
NM_022566.3 synonymous
NM_022566.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.17
Genes affected
TLNRD1 (HGNC:13519): (talin rod domain containing 1) This gene encodes a protein that is regulated by micro RNA MiR-574-3, and is thought to have an oncogenic function in human bladder cancer. A similar gene in mouse is located in a chromosomal region critical for differentiation of mesoderm, which affects embryo patterning and the formation of heart, muscle, blood, skeleton and the urogenital system. The mouse gene is expressed in early development, and in the adult. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 15-81002887-C-A is Benign according to our data. Variant chr15-81002887-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2645632.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.16 with no splicing effect.
BS2
High AC in GnomAd4 at 215 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLNRD1 | NM_022566.3 | c.616C>A | p.Arg206= | synonymous_variant | 1/1 | ENST00000267984.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLNRD1 | ENST00000267984.4 | c.616C>A | p.Arg206= | synonymous_variant | 1/1 | NM_022566.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152218Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000334 AC: 76AN: 227738Hom.: 1 AF XY: 0.000223 AC XY: 28AN XY: 125346
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GnomAD4 exome AF: 0.000138 AC: 200AN: 1444906Hom.: 1 Cov.: 31 AF XY: 0.000121 AC XY: 87AN XY: 719154
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GnomAD4 genome AF: 0.00141 AC: 215AN: 152328Hom.: 2 Cov.: 33 AF XY: 0.00141 AC XY: 105AN XY: 74488
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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 | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | TLNRD1: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at