rs55983148
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-A
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
- chr11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_153676.4(USH1C):c.496+21_497-73delGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000045 in 887,946 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000015 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000037 ( 0 hom. )
Consequence
USH1C
NM_153676.4 intron
NM_153676.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.428
Publications
0 publications found
Genes affected
USH1C (HGNC:12597): (USH1 protein network component harmonin) This gene encodes a scaffold protein that functions in the assembly of Usher protein complexes. The protein contains PDZ domains, a coiled-coil region with a bipartite nuclear localization signal and a PEST degradation sequence. Defects in this gene are the cause of Usher syndrome type 1C and non-syndromic sensorineural deafness autosomal recessive type 18. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]
USH1C Gene-Disease associations (from GenCC):
- Usher syndrome type 1Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- Usher syndrome type 1CInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics, PanelApp Australia
- autosomal recessive nonsyndromic hearing loss 18AInheritance: AR, Unknown Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
- hearing loss, autosomal recessiveInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- nonsyndromic genetic hearing lossInheritance: AR Classification: LIMITED Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| USH1C | NM_153676.4 | c.496+21_497-73delGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG | intron_variant | Intron 5 of 26 | ENST00000005226.12 | NP_710142.1 | ||
| USH1C | NM_005709.4 | c.496+21_497-73delGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG | intron_variant | Intron 5 of 20 | ENST00000318024.9 | NP_005700.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| USH1C | ENST00000005226.12 | c.496+21_497-73delGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG | intron_variant | Intron 5 of 26 | 5 | NM_153676.4 | ENSP00000005226.7 | |||
| USH1C | ENST00000318024.9 | c.496+21_497-73delGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG | intron_variant | Intron 5 of 20 | 1 | NM_005709.4 | ENSP00000317018.4 |
Frequencies
GnomAD3 genomes 0.0000150 AC: 1AN: 66622Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
66622
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000365 AC: 3AN: 821324Hom.: 0 AF XY: 0.00000491 AC XY: 2AN XY: 407178 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
821324
Hom.:
AF XY:
AC XY:
2
AN XY:
407178
show subpopulations
African (AFR)
AF:
AC:
0
AN:
18892
American (AMR)
AF:
AC:
1
AN:
25030
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17330
East Asian (EAS)
AF:
AC:
1
AN:
28598
South Asian (SAS)
AF:
AC:
0
AN:
50968
European-Finnish (FIN)
AF:
AC:
0
AN:
30070
Middle Eastern (MID)
AF:
AC:
0
AN:
2720
European-Non Finnish (NFE)
AF:
AC:
1
AN:
612606
Other (OTH)
AF:
AC:
0
AN:
35110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.642
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.0000150 AC: 1AN: 66622Hom.: 0 Cov.: 0 AF XY: 0.0000325 AC XY: 1AN XY: 30732 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
66622
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
30732
show subpopulations
African (AFR)
AF:
AC:
0
AN:
17272
American (AMR)
AF:
AC:
0
AN:
6350
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2010
East Asian (EAS)
AF:
AC:
1
AN:
2424
South Asian (SAS)
AF:
AC:
0
AN:
1538
European-Finnish (FIN)
AF:
AC:
0
AN:
3582
Middle Eastern (MID)
AF:
AC:
0
AN:
136
European-Non Finnish (NFE)
AF:
AC:
0
AN:
32118
Other (OTH)
AF:
AC:
0
AN:
832
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.725
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.