rs145598174
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000601.6(HGF):āc.270T>Gā(p.Asp90Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,458,706 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes š: 6.9e-7 ( 0 hom. )
Consequence
HGF
NM_000601.6 missense
NM_000601.6 missense
Scores
8
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.667
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1458706Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725912
GnomAD4 exome
AF:
AC:
1
AN:
1458706
Hom.:
Cov.:
29
AF XY:
AC XY:
0
AN XY:
725912
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 NFE exome
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Gnomad4 OTH exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;D;.;.;.;.;.;D;D;.;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
.;T;T;T;T;T;T;T;T;T;T
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M;M;M;M;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;N;N;N;.;N;.;N;D
REVEL
Uncertain
Sift
Benign
.;T;T;T;T;T;.;T;.;D;D
Sift4G
Benign
.;T;T;T;T;T;.;D;.;.;.
Polyphen
D;D;D;D;D;.;.;.;.;.;.
Vest4
0.23, 0.21, 0.21, 0.21, 0.21, 0.20
MutPred
Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);Loss of MoRF binding (P = 0.0908);
MVP
0.84
MPC
0.47
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.