NM_000327.4:c.2dupT
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_000327.4(ROM1):c.2dupT(p.Met1IlefsTer39) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,170 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 34)
Consequence
ROM1
NM_000327.4 frameshift, start_lost
NM_000327.4 frameshift, start_lost
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.46
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- retinitis pigmentosa 7Inheritance: AD, Unknown Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
- retinitis pigmentosaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000327.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ROM1 | NM_000327.4 | MANE Select | c.2dupT | p.Met1IlefsTer39 | frameshift start_lost | Exon 1 of 3 | NP_000318.2 | Q03395 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ROM1 | ENST00000278833.4 | TSL:1 MANE Select | c.2dupT | p.Met1IlefsTer39 | frameshift start_lost | Exon 1 of 3 | ENSP00000278833.3 | Q03395 | |
| ROM1 | ENST00000534093.5 | TSL:2 | c.-38-975dupT | intron | N/A | ENSP00000432151.1 | E9PS24 | ||
| ROM1 | ENST00000525801.1 | TSL:3 | c.-38-975dupT | intron | N/A | ENSP00000433566.1 | E9PKF5 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152170
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Cov.: 77
GnomAD4 exome
Cov.:
77
GnomAD4 genome 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152170
Hom.:
Cov.:
34
AF XY:
AC XY:
1
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41426
American (AMR)
AF:
AC:
0
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
0
AN:
4826
European-Finnish (FIN)
AF:
AC:
0
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68020
Other (OTH)
AF:
AC:
0
AN:
2092
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.