7-81702807-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000601.6(HGF):c.2011-50C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 1,474,030 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0024 ( 8 hom. )
Consequence
HGF
NM_000601.6 intron
NM_000601.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0320
Genes affected
HGF (HGNC:4893): (hepatocyte growth factor) This gene encodes a protein that binds to the hepatocyte growth factor receptor to regulate cell growth, cell motility and morphogenesis in numerous cell and tissue types. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate alpha and beta chains, which form the mature heterodimer. This protein is secreted by mesenchymal cells and acts as a multi-functional cytokine on cells of mainly epithelial origin. This protein also plays a role in angiogenesis, tumorogenesis, and tissue regeneration. Although the encoded protein is a member of the peptidase S1 family of serine proteases, it lacks peptidase activity. Mutations in this gene are associated with nonsyndromic hearing loss. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 7-81702807-G-T is Benign according to our data. Variant chr7-81702807-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1186051.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HGF | NM_000601.6 | c.2011-50C>A | intron_variant | ENST00000222390.11 | NP_000592.3 | |||
HGF | NM_001010932.3 | c.1996-50C>A | intron_variant | NP_001010932.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HGF | ENST00000222390.11 | c.2011-50C>A | intron_variant | 1 | NM_000601.6 | ENSP00000222390 | P4 | |||
HGF | ENST00000457544.7 | c.1996-50C>A | intron_variant | 1 | ENSP00000391238 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 286AN: 151420Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00242 AC: 580AN: 240076Hom.: 2 AF XY: 0.00257 AC XY: 336AN XY: 130646
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GnomAD4 exome AF: 0.00240 AC: 3177AN: 1322492Hom.: 8 Cov.: 21 AF XY: 0.00244 AC XY: 1624AN XY: 665698
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GnomAD4 genome AF: 0.00189 AC: 286AN: 151538Hom.: 0 Cov.: 32 AF XY: 0.00189 AC XY: 140AN XY: 74060
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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 | GeneDx | Jun 12, 2020 | - - |
Computational scores
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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