7-81705697-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_000601.6(HGF):c.1814C>T(p.Thr605Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00017 in 1,612,482 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000601.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HGF | NM_000601.6 | c.1814C>T | p.Thr605Ile | missense_variant | 16/18 | ENST00000222390.11 | |
HGF | NM_001010932.3 | c.1799C>T | p.Thr600Ile | missense_variant | 16/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HGF | ENST00000222390.11 | c.1814C>T | p.Thr605Ile | missense_variant | 16/18 | 1 | NM_000601.6 | P4 | |
HGF | ENST00000457544.7 | c.1799C>T | p.Thr600Ile | missense_variant | 16/18 | 1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000659 AC: 10AN: 151812Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000719 AC: 18AN: 250428Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135326
GnomAD4 exome AF: 0.000181 AC: 264AN: 1460670Hom.: 1 Cov.: 30 AF XY: 0.000172 AC XY: 125AN XY: 726664
GnomAD4 genome AF: 0.0000659 AC: 10AN: 151812Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74134
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 11, 2015 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 26, 2015 | p.Thr605Ile in exon 16 of HGF: This variant is not expected to have clinical sig nificance due to a lack of conservation across species, including mammals. Of no te, 3 mammals (rabbit, David's myotis and big brown bat) have an isoleucine (Ile ) at this position despite high nearby amino acid conservation. In addition, it has also been identified in 6/66144 of European chromosomes by the Exome Aggrega tion Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs147075806). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at