Variant 3-150927631-TACAC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_174878.3(CLRN1):c.*301_*304del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 457,236 control chromosomes in the GnomAD database, including 1,686 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.10 ( 875 hom., cov: 0)

Exomes 𝑓: 0.12 ( 811 hom. )

Consequence

CLRN1
NM_174878.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:1

Conservation

PhyloP100: -0.0270

Variant links:

Genes affected

CLRN1 (HGNC:12605): (clarin 1) This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

CLRN1 links:

(HGNC:):

links:

CLRN1-AS1 (HGNC:30895): (CLRN1 antisense RNA 1)

CLRN1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 3-150927631-TACAC-T is Benign according to our data. Variant chr3-150927631-TACAC-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 343810.We mark this variant Likely_benign, oryginal submissions are: {Benign=1, Uncertain_significance=2}.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLRN1	NM_174878.3 linkuse as main transcript	c.301_304del		3_prime_UTR_variant	3/3	ENST00000327047.6	NP_777367.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLRN1	ENST00000327047.6 linkuse as main transcript	c.301_304del	3_prime_UTR_variant	3/3	1	NM_174878.3	ENSP00000322280	P1	P58418-3
CLRN1	ENST00000295911.6 linkuse as main transcript	c.342+430_342+433del	intron_variant		1		ENSP00000295911		P58418-1
	ENST00000469268.1 linkuse as main transcript	n.235+36787_235+36790del	intron_variant, non_coding_transcript_variant		4
CLRN1-AS1	ENST00000476886.5 linkuse as main transcript	n.123+75051_123+75054del	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

14909

AN:

148482

Hom.:

873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.0615

Gnomad AMR

AF:

0.129

Gnomad ASJ

AF:

0.0679

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.0676

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.103

Gnomad NFE

AF:

0.0730

Gnomad OTH

AF:

0.0953

GnomAD3 exomes

AF:

0.146

AC:

14560

AN:

99722

Hom.:

282

AF XY:

0.140

AC XY:

7623

AN XY:

54260

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.100

Gnomad EAS exome

AF:

0.300

Gnomad SAS exome

AF:

0.0989

Gnomad FIN exome

AF:

0.158

Gnomad NFE exome

AF:

0.121

Gnomad OTH exome

AF:

0.139

GnomAD4 exome

AF:

0.121

AC:

37338

AN:

308642

Hom.:

811

AF XY:

0.117

AC XY:

20215

AN XY:

172620

show subpopulations

Gnomad4 AFR exome

AF:

0.145

Gnomad4 AMR exome

AF:

0.168

Gnomad4 ASJ exome

AF:

0.0889

Gnomad4 EAS exome

AF:

0.277

Gnomad4 SAS exome

AF:

0.0912

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.129

GnomAD4 genome

AF:

0.100

AC:

14928

AN:

148594

Hom.:

875

Cov.:

AF XY:

0.104

AC XY:

7546

AN XY:

72320

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.129

Gnomad4 ASJ

AF:

0.0679

Gnomad4 EAS

AF:

0.273

Gnomad4 SAS

AF:

0.0681

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.0730

Gnomad4 OTH

AF:

0.0968

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Retinitis pigmentosa-deafness syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Retinitis Pigmentosa, Dominant

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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