5-80058361-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003248.6(THBS4):c.649+47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,393,678 control chromosomes in the GnomAD database, including 70,061 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.30 ( 7065 hom., cov: 32)
Exomes 𝑓: 0.32 ( 62996 hom. )
Consequence
THBS4
NM_003248.6 intron
NM_003248.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.470
Genes affected
THBS4 (HGNC:11788): (thrombospondin 4) The protein encoded by this gene belongs to the thrombospondin protein family. Thrombospondin family members are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. This protein forms a pentamer and can bind to heparin and calcium. It is involved in local signaling in the developing and adult nervous system, and it contributes to spinal sensitization and neuropathic pain states. This gene is activated during the stromal response to invasive breast cancer. It may also play a role in inflammatory responses in Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THBS4 | NM_003248.6 | c.649+47A>G | intron_variant | ENST00000350881.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THBS4 | ENST00000350881.6 | c.649+47A>G | intron_variant | 1 | NM_003248.6 | P1 | |||
THBS4-AS1 | ENST00000503007.5 | n.429-5460T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
THBS4 | ENST00000511733.1 | c.376+47A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.301 AC: 45736AN: 152050Hom.: 7051 Cov.: 32
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GnomAD3 exomes AF: 0.290 AC: 42698AN: 147028Hom.: 6262 AF XY: 0.293 AC XY: 22773AN XY: 77790
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GnomAD4 exome AF: 0.317 AC: 393704AN: 1241510Hom.: 62996 Cov.: 17 AF XY: 0.315 AC XY: 194655AN XY: 617578
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GnomAD4 genome AF: 0.301 AC: 45790AN: 152168Hom.: 7065 Cov.: 32 AF XY: 0.296 AC XY: 22037AN XY: 74378
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ClinVar
Not reported inComputational 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