11-17527112-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC

Variant names:

• chr11-17527112-A-ACCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGCCCTGCTCCCCCGCCCTCCCTCCCTCCCACCGTCATGGAGTACTGC
• rs55983148
• NM_153676.4:c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_153676.4(USH1C):​c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000122 in 821,322 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 INS_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: not found (cov: 0)
  • Exomes 𝑓: 0.0000012 (0 hom.)
• Consequence: USH1C NM_153676.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• 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 1C

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
• Usher syndrome type 1

  Inheritance: Unknown, AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• autosomal recessive nonsyndromic hearing loss 18A

  Inheritance: AR, Unknown Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153676.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USH1C	NM_153676.4	MANE Select	c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	NP_710142.1	Q9Y6N9-5
	USH1C	NM_005709.4	MANE Plus Clinical	c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	NP_005700.2	A0A0S2Z4U9
	USH1C	NM_001440679.1		c.530-73_530-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	NP_001427608.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	USH1C	ENST00000005226.12	TSL:5 MANE Select	c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	ENSP00000005226.7	Q9Y6N9-5
	USH1C	ENST00000318024.9	TSL:1 MANE Plus Clinical	c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	ENSP00000317018.4	Q9Y6N9-1
	USH1C	ENST00000527020.5	TSL:1	c.497-73_497-72insGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGGGCAGTACTCCATGACGGTGGGAGGGAGGGAGGGCGGGGGAGCAGG		intron	N/A	ENSP00000436934.1	Q9Y6N9-4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000122 AC: 1 AN: 821322 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 407176

African (AFR) AF: 0.00 AC: 0 AN: 18892

American (AMR) AF: 0.00 AC: 0 AN: 25030

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17330

East Asian (EAS) AF: 0.0000350 AC: 1 AN: 28596

South Asian (SAS) AF: 0.00 AC: 0 AN: 50968

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30070

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2720

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 612606

Other (OTH) AF: 0.00 AC: 0 AN: 35110

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55983148;

hg19: chr11-17548659;