Variant chr11-17533369-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000527720.5(USH1C):c.-104G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,379,894 control chromosomes in the GnomAD database, including 12,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 982 hom., cov: 31)

Exomes 𝑓: 0.12 ( 11686 hom. )

Consequence

USH1C
ENST00000527720.5 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.769

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 11-17533369-C-A is Benign according to our data. Variant chr11-17533369-C-A is described in ClinVar as [Benign]. Clinvar id is 262735.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-17533369-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USH1C	NM_005709.4 linkuse as main transcript	c.37-47G>T		intron_variant		ENST00000318024.9
USH1C	NM_153676.4 linkuse as main transcript	c.37-47G>T		intron_variant		ENST00000005226.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USH1C	ENST00000005226.12 linkuse as main transcript	c.37-47G>T		intron_variant		5	NM_153676.4		Q9Y6N9-5
USH1C	ENST00000318024.9 linkuse as main transcript	c.37-47G>T		intron_variant		1	NM_005709.4	P1	Q9Y6N9-1

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15345

AN:

146812

Hom.:

980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0712

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0860

Gnomad ASJ

AF:

0.0852

Gnomad EAS

AF:

0.0637

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.138

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.0968

GnomAD3 exomes

AF:

0.126

AC:

29540

AN:

233934

Hom.:

2703

AF XY:

0.134

AC XY:

17113

AN XY:

127420

show subpopulations

Gnomad AFR exome

AF:

0.0771

Gnomad AMR exome

AF:

0.0743

Gnomad ASJ exome

AF:

0.0942

Gnomad EAS exome

AF:

0.0595

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.141

Gnomad NFE exome

AF:

0.120

Gnomad OTH exome

AF:

0.127

GnomAD4 exome

AF:

0.125

AC:

153849

AN:

1232970

Hom.:

11686

Cov.:

AF XY:

0.129

AC XY:

80407

AN XY:

625138

show subpopulations

Gnomad4 AFR exome

AF:

0.0625

Gnomad4 AMR exome

AF:

0.0756

Gnomad4 ASJ exome

AF:

0.0903

Gnomad4 EAS exome

AF:

0.0580

Gnomad4 SAS exome

AF:

0.265

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.120

Gnomad4 OTH exome

AF:

0.128

GnomAD4 genome

AF:

0.104

AC:

15346

AN:

146924

Hom.:

982

Cov.:

AF XY:

0.108

AC XY:

7736

AN XY:

71818

show subpopulations

Gnomad4 AFR

AF:

0.0710

Gnomad4 AMR

AF:

0.0859

Gnomad4 ASJ

AF:

0.0852

Gnomad4 EAS

AF:

0.0637

Gnomad4 SAS

AF:

0.263

Gnomad4 FIN

AF:

0.137

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.0997

Alfa

AF:

0.0104

Hom.:

Bravo

AF:

0.111

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 16, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Autosomal recessive nonsyndromic hearing loss 18A

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 10, 2021

- -

Usher syndrome type 1C

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

DANN

Benign

0.45

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over