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

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_174878.3(CLRN1):c.*303_*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 0.473 in 462,398 control chromosomes in the GnomAD database, including 34,704 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 21173 hom., cov: 0)

Exomes 𝑓: 0.44 ( 13531 hom. )

Consequence

CLRN1
NM_174878.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

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 -16 ACMG points.

BP6

Variant 3-150927631-TAC-T is Benign according to our data. Variant chr3-150927631-TAC-T is described in ClinVar as [Benign]. Clinvar id is 343809.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 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.303_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.303_304del	3_prime_UTR_variant	3/3	1	NM_174878.3	ENSP00000322280	P1	P58418-3
CLRN1	ENST00000295911.6 linkuse as main transcript	c.342+432_342+433del	intron_variant		1		ENSP00000295911		P58418-1
	ENST00000469268.1 linkuse as main transcript	n.235+36789_235+36790del	intron_variant, non_coding_transcript_variant		4
CLRN1-AS1	ENST00000476886.5 linkuse as main transcript	n.123+75053_123+75054del	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

79355

AN:

148458

Hom.:

21176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.495

Gnomad AMI

AF:

0.643

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.513

Gnomad SAS

AF:

0.496

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.521

GnomAD3 exomes

AF:

0.444

AC:

44311

AN:

99722

Hom.:

3366

AF XY:

0.445

AC XY:

24142

AN XY:

54260

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.410

Gnomad ASJ exome

AF:

0.427

Gnomad EAS exome

AF:

0.429

Gnomad SAS exome

AF:

0.428

Gnomad FIN exome

AF:

0.432

Gnomad NFE exome

AF:

0.480

Gnomad OTH exome

AF:

0.456

GnomAD4 exome

AF:

0.444

AC:

139490

AN:

313830

Hom.:

13531

AF XY:

0.443

AC XY:

77508

AN XY:

175136

show subpopulations

Gnomad4 AFR exome

AF:

0.417

Gnomad4 AMR exome

AF:

0.403

Gnomad4 ASJ exome

AF:

0.403

Gnomad4 EAS exome

AF:

0.426

Gnomad4 SAS exome

AF:

0.412

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.467

Gnomad4 OTH exome

AF:

0.449

GnomAD4 genome

AF:

0.534

AC:

79384

AN:

148568

Hom.:

21173

Cov.:

AF XY:

0.529

AC XY:

38259

AN XY:

72320

show subpopulations

Gnomad4 AFR

AF:

0.494

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.454

Gnomad4 EAS

AF:

0.512

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.512

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.521

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 08, 2019

- -

Retinitis pigmentosa-deafness syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Retinitis Pigmentosa, Dominant

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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