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GeneBe

11-62613297-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000327.4(ROM1):c.16C>T(p.Pro6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ROM1
NM_000327.4 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0470
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.078671694).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ROM1NM_000327.4 linkuse as main transcriptc.16C>T p.Pro6Ser missense_variant 1/3 ENST00000278833.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ROM1ENST00000278833.4 linkuse as main transcriptc.16C>T p.Pro6Ser missense_variant 1/31 NM_000327.4 P1
ROM1ENST00000525801.1 linkuse as main transcriptc.-38-961C>T intron_variant 3
ROM1ENST00000534093.5 linkuse as main transcriptc.-38-961C>T intron_variant 2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1455132
Hom.:
0
Cov.:
77
AF XY:
0.00
AC XY:
0
AN XY:
723618
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2022ROM1: PM2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.60
Cadd
Benign
20
Dann
Uncertain
0.99
DEOGEN2
Benign
0.31
T
Eigen
Benign
-0.26
Eigen_PC
Benign
-0.20
FATHMM_MKL
Benign
0.45
N
LIST_S2
Benign
0.74
T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.079
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
1.2
L
MutationTaster
Benign
1.0
D;N
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-0.76
N
REVEL
Benign
0.042
Sift
Benign
0.079
T
Sift4G
Benign
0.22
T
Polyphen
0.44
B
Vest4
0.21
MutPred
0.41
Gain of sheet (P = 0.0344);
MVP
0.32
MPC
0.048
ClinPred
0.57
D
GERP RS
3.2
Varity_R
0.096
gMVP
0.40

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-62380769; API