rs2166975
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_003236.4(TGFA):c.480C>T(p.Val160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,607,768 control chromosomes in the GnomAD database, including 57,977 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 0.23 ( 4518 hom., cov: 32)
Exomes 𝑓: 0.27 ( 53459 hom. )
Consequence
TGFA
NM_003236.4 synonymous
NM_003236.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.02
Genes affected
TGFA (HGNC:11765): (transforming growth factor alpha) This gene encodes a growth factor that is a ligand for the epidermal growth factor receptor, which activates a signaling pathway for cell proliferation, differentiation and development. This protein may act as either a transmembrane-bound ligand or a soluble ligand. This gene has been associated with many types of cancers, and it may also be involved in some cases of cleft lip/palate. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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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=-0.52).
BP7
?
Synonymous conserved (PhyloP=2.03 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFA | NM_003236.4 | c.480C>T | p.Val160= | synonymous_variant | 6/6 | ENST00000295400.11 | |
TGFA | NM_001308158.2 | c.498C>T | p.Val166= | synonymous_variant | 6/6 | ||
TGFA | NM_001308159.2 | c.495C>T | p.Val165= | synonymous_variant | 6/6 | ||
TGFA | NM_001099691.3 | c.477C>T | p.Val159= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFA | ENST00000295400.11 | c.480C>T | p.Val160= | synonymous_variant | 6/6 | 1 | NM_003236.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35557AN: 151954Hom.: 4510 Cov.: 32
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GnomAD3 exomes AF: 0.240 AC: 58120AN: 242456Hom.: 7581 AF XY: 0.244 AC XY: 31952AN XY: 130752
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GnomAD4 exome AF: 0.267 AC: 388789AN: 1455696Hom.: 53459 Cov.: 33 AF XY: 0.266 AC XY: 192735AN XY: 723506
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GnomAD4 genome ? AF: 0.234 AC: 35575AN: 152072Hom.: 4518 Cov.: 32 AF XY: 0.234 AC XY: 17378AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at