NM_004560.4:c.97+43416A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004560.4(ROR2):c.97+43416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,044 control chromosomes in the GnomAD database, including 4,866 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 4866 hom., cov: 32)
Consequence
ROR2
NM_004560.4 intron
NM_004560.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.23
Publications
8 publications found
Genes affected
ROR2 (HGNC:10257): (receptor tyrosine kinase like orphan receptor 2) The protein encoded by this gene is a receptor protein tyrosine kinase and type I transmembrane protein that belongs to the ROR subfamily of cell surface receptors. The protein may be involved in the early formation of the chondrocytes and may be required for cartilage and growth plate development. Mutations in this gene can cause brachydactyly type B, a skeletal disorder characterized by hypoplasia/aplasia of distal phalanges and nails. In addition, mutations in this gene can cause the autosomal recessive form of Robinow syndrome, which is characterized by skeletal dysplasia with generalized limb bone shortening, segmental defects of the spine, brachydactyly, and a dysmorphic facial appearance. [provided by RefSeq, Jul 2008]
ROR2 Gene-Disease associations (from GenCC):
- brachydactyly type B1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- autosomal recessive Robinow syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ROR2 | ENST00000375708.4 | c.97+43416A>G | intron_variant | Intron 1 of 8 | 1 | NM_004560.4 | ENSP00000364860.3 | |||
ROR2 | ENST00000375715.5 | c.-324+42156A>G | intron_variant | Intron 1 of 12 | 1 | ENSP00000364867.1 | ||||
ROR2 | ENST00000495386.5 | n.234+17314A>G | intron_variant | Intron 2 of 4 | 3 | |||||
ROR2 | ENST00000546883.1 | n.299+17314A>G | intron_variant | Intron 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.236 AC: 35851AN: 151926Hom.: 4859 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
35851
AN:
151926
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.236 AC: 35862AN: 152044Hom.: 4866 Cov.: 32 AF XY: 0.243 AC XY: 18072AN XY: 74324 show subpopulations
GnomAD4 genome
AF:
AC:
35862
AN:
152044
Hom.:
Cov.:
32
AF XY:
AC XY:
18072
AN XY:
74324
show subpopulations
African (AFR)
AF:
AC:
5242
AN:
41490
American (AMR)
AF:
AC:
6454
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
847
AN:
3470
East Asian (EAS)
AF:
AC:
1935
AN:
5152
South Asian (SAS)
AF:
AC:
1221
AN:
4806
European-Finnish (FIN)
AF:
AC:
2893
AN:
10564
Middle Eastern (MID)
AF:
AC:
53
AN:
294
European-Non Finnish (NFE)
AF:
AC:
16505
AN:
67992
Other (OTH)
AF:
AC:
483
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
1316
2633
3949
5266
6582
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
370
740
1110
1480
1850
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1064
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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.