Variant chr11-62612953-G-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 ENST00000534093.5(ROM1):c.-39+1033G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 438,270 control chromosomes in the GnomAD database, including 12,529 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 3766 hom., cov: 33)

Exomes 𝑓: 0.23 ( 8763 hom. )

Consequence

ROM1
ENST00000534093.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0590

Variant links:

Genes affected

ROM1 (HGNC:10254): (retinal outer segment membrane protein 1) This gene is a member of a photoreceptor-specific gene family and encodes an integral membrane protein found in the photoreceptor disk rim of the eye. This protein can form homodimers or can heterodimerize with another photoreceptor, retinal degeneration slow (RDS). It is essential for disk morphogenesis, and may also function as an adhesion molecule involved in the stabilization and compaction of outer segment disks or in the maintenance of the curvature of the rim. Certain defects in this gene have been associated with the degenerative eye disease retinitis pigmentosa. [provided by RefSeq, Jul 2008]

ROM1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 11-62612953-G-T is Benign according to our data. Variant chr11-62612953-G-T is described in ClinVar as [Benign]. Clinvar id is 305156.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROM1	ENST00000525801.1 linkuse as main transcript	c.-39+862G>T		intron_variant		3
ROM1	ENST00000534093.5 linkuse as main transcript	c.-39+1033G>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31755

AN:

151768

Hom.:

3762

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.0519

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.283

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.233

AC:

66659

AN:

286388

Hom.:

8763

Cov.:

AF XY:

0.229

AC XY:

34266

AN XY:

149576

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.263

Gnomad4 EAS exome

AF:

0.0493

Gnomad4 SAS exome

AF:

0.170

Gnomad4 FIN exome

AF:

0.198

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.209

AC:

31768

AN:

151882

Hom.:

3766

Cov.:

AF XY:

0.204

AC XY:

15163

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.136

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.259

Gnomad4 EAS

AF:

0.0518

Gnomad4 SAS

AF:

0.159

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.236

Alfa

AF:

0.240

Hom.:

615

Bravo

AF:

0.205

Asia WGS

AF:

0.109

AC:

384

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Retinitis pigmentosa

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.1

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.58

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.58

Position offset: -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