15-39581891-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_003246.4(THBS1):c.34C>T(p.Leu12=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 1,614,090 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 33 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 41 hom. )
Consequence
THBS1
NM_003246.4 synonymous
NM_003246.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.61
Genes affected
THBS1 (HGNC:11785): (thrombospondin 1) The protein encoded by this gene is a subunit of a disulfide-linked homotrimeric protein. This protein is an adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. This protein can bind to fibrinogen, fibronectin, laminin, type V collagen and integrins alpha-V/beta-1. This protein has been shown to play roles in platelet aggregation, angiogenesis, and tumorigenesis. [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=-0.36).
BP6
?
Variant 15-39581891-C-T is Benign according to our data. Variant chr15-39581891-C-T is described in ClinVar as [Benign]. Clinvar id is 783705.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.61 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0125 (1900/152224) while in subpopulation AFR AF= 0.0438 (1819/41518). AF 95% confidence interval is 0.0421. There are 33 homozygotes in gnomad4. There are 902 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1893 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.34C>T | p.Leu12= | synonymous_variant | 2/22 | ENST00000260356.6 | |
THBS1 | XM_047432980.1 | c.34C>T | p.Leu12= | synonymous_variant | 2/22 | ||
THBS1 | XM_011521971.3 | c.34C>T | p.Leu12= | synonymous_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS1 | ENST00000260356.6 | c.34C>T | p.Leu12= | synonymous_variant | 2/22 | 1 | NM_003246.4 | P1 | |
THBS1 | ENST00000397591.2 | c.34C>T | p.Leu12= | synonymous_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0124 AC: 1893AN: 152106Hom.: 33 Cov.: 32
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GnomAD3 exomes AF: 0.00297 AC: 747AN: 251358Hom.: 13 AF XY: 0.00209 AC XY: 284AN XY: 135844
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GnomAD4 exome AF: 0.00127 AC: 1860AN: 1461866Hom.: 41 Cov.: 31 AF XY: 0.00111 AC XY: 805AN XY: 727236
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GnomAD4 genome ? AF: 0.0125 AC: 1900AN: 152224Hom.: 33 Cov.: 32 AF XY: 0.0121 AC XY: 902AN XY: 74416
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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 | Dec 31, 2019 | - - |
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