7-81702807-G-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0320
Variant links:
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
HGFNM_000601.6 linkuse as main transcriptc.2011-50C>A intron_variant ENST00000222390.11 NP_000592.3
HGFNM_001010932.3 linkuse as main transcriptc.1996-50C>A intron_variant NP_001010932.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HGFENST00000222390.11 linkuse as main transcriptc.2011-50C>A intron_variant 1 NM_000601.6 ENSP00000222390 P4P14210-1
HGFENST00000457544.7 linkuse as main transcriptc.1996-50C>A intron_variant 1 ENSP00000391238 A1P14210-3

Frequencies

GnomAD3 genomes
AF:
0.00189
AC:
286
AN:
151420
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000387
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00258
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00125
Gnomad FIN
AF:
0.00274
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00282
Gnomad OTH
AF:
0.00240
GnomAD3 exomes
AF:
0.00242
AC:
580
AN:
240076
Hom.:
2
AF XY:
0.00257
AC XY:
336
AN XY:
130646
show subpopulations
Gnomad AFR exome
AF:
0.000411
Gnomad AMR exome
AF:
0.00438
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000577
Gnomad SAS exome
AF:
0.000571
Gnomad FIN exome
AF:
0.00216
Gnomad NFE exome
AF:
0.00320
Gnomad OTH exome
AF:
0.00307
GnomAD4 exome
AF:
0.00240
AC:
3177
AN:
1322492
Hom.:
8
Cov.:
21
AF XY:
0.00244
AC XY:
1624
AN XY:
665698
show subpopulations
Gnomad4 AFR exome
AF:
0.000333
Gnomad4 AMR exome
AF:
0.00431
Gnomad4 ASJ exome
AF:
0.0000399
Gnomad4 EAS exome
AF:
0.0000261
Gnomad4 SAS exome
AF:
0.000896
Gnomad4 FIN exome
AF:
0.00283
Gnomad4 NFE exome
AF:
0.00265
Gnomad4 OTH exome
AF:
0.00219
GnomAD4 genome
AF:
0.00189
AC:
286
AN:
151538
Hom.:
0
Cov.:
32
AF XY:
0.00189
AC XY:
140
AN XY:
74060
show subpopulations
Gnomad4 AFR
AF:
0.000386
Gnomad4 AMR
AF:
0.00258
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.00274
Gnomad4 NFE
AF:
0.00282
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00202
Hom.:
0
Bravo
AF:
0.00193
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

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 submitterclinical testingGeneDxJun 12, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.47
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs78291552; hg19: chr7-81332123; API