NM_173477.5:c.96C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_173477.5(USH1G):c.96C>T(p.Gly32Gly) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000657 in 152,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
USH1G
NM_173477.5 synonymous
NM_173477.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.11
Publications
0 publications found
Genes affected
USH1G (HGNC:16356): (USH1 protein network component sans) This gene encodes a protein that contains three ankyrin domains, a class I PDZ-binding motif and a sterile alpha motif. The encoded protein interacts with harmonin, which is associated with Usher syndrome type 1C. This protein plays a role in the development and maintenance of the auditory and visual systems and functions in the cohesion of hair bundles formed by inner ear sensory cells. Mutations in this gene are associated with Usher syndrome type 1G (USH1G). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
OTOP2 (HGNC:19657): (otopetrin 2) Predicted to enable proton channel activity. Predicted to be involved in proton transmembrane transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 17-74922978-G-A is Benign according to our data. Variant chr17-74922978-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2033579.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| USH1G | NM_173477.5 | c.96C>T | p.Gly32Gly | synonymous_variant | Exon 1 of 3 | ENST00000614341.5 | NP_775748.2 | |
| USH1G | NM_001282489.3 | c.-161C>T | 5_prime_UTR_variant | Exon 1 of 3 | NP_001269418.1 | |||
| USH1G | XM_011524296.2 | c.-548C>T | upstream_gene_variant | XP_011522598.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| USH1G | ENST00000614341.5 | c.96C>T | p.Gly32Gly | synonymous_variant | Exon 1 of 3 | 1 | NM_173477.5 | ENSP00000480279.1 | ||
| OTOP2 | ENST00000580223.2 | c.-287G>A | 5_prime_UTR_variant | Exon 1 of 5 | 1 | ENSP00000463837.2 | ||||
| USH1G | ENST00000579243.1 | n.96C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | ENSP00000462568.1 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152216
Hom.:
Cov.:
30
Gnomad AFR
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000577 AC: 1AN: 173184 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
173184
AF XY:
Gnomad AFR exome
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1407000Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 694318
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1407000
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
694318
African (AFR)
AF:
AC:
0
AN:
32144
American (AMR)
AF:
AC:
0
AN:
37314
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25202
East Asian (EAS)
AF:
AC:
0
AN:
36636
South Asian (SAS)
AF:
AC:
0
AN:
80102
European-Finnish (FIN)
AF:
AC:
0
AN:
49504
Middle Eastern (MID)
AF:
AC:
0
AN:
5652
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1082190
Other (OTH)
AF:
AC:
0
AN:
58256
GnomAD4 genome 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74356 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152216
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
74356
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41466
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5188
South Asian (SAS)
AF:
AC:
0
AN:
4822
European-Finnish (FIN)
AF:
AC:
0
AN:
10626
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68028
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 01, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
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