rs2286194
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000601.6(HGF):c.1041-116A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,035,140 control chromosomes in the GnomAD database, including 20,588 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.19 ( 2996 hom., cov: 32)
Exomes 𝑓: 0.20 ( 17592 hom. )
Consequence
HGF
NM_000601.6 intron
NM_000601.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.284
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
?
Variant 7-81726133-T-A is Benign according to our data. Variant chr7-81726133-T-A is described in ClinVar as [Benign]. Clinvar id is 1261544.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-81726133-T-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGF | NM_000601.6 | c.1041-116A>T | intron_variant | ENST00000222390.11 | |||
HGF | NM_001010932.3 | c.1026-116A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGF | ENST00000222390.11 | c.1041-116A>T | intron_variant | 1 | NM_000601.6 | P4 | |||
HGF | ENST00000457544.7 | c.1026-116A>T | intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.195 AC: 29636AN: 152094Hom.: 2994 Cov.: 32
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GnomAD4 exome AF: 0.197 AC: 174012AN: 882928Hom.: 17592 AF XY: 0.201 AC XY: 92673AN XY: 460420
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GnomAD4 genome ? AF: 0.195 AC: 29651AN: 152212Hom.: 2996 Cov.: 32 AF XY: 0.194 AC XY: 14407AN XY: 74426
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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 | GeneDx | Dec 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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