1-186401059-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017847.6(ODR4):c.1000+2015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000346 in 1,443,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
ODR4
NM_017847.6 intron
NM_017847.6 intron
Scores
1
9
Clinical Significance
Conservation
PhyloP100: -0.644
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05830592).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ODR4 | NM_017847.6 | c.1000+2015C>T | intron_variant | ENST00000287859.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ODR4 | ENST00000287859.11 | c.1000+2015C>T | intron_variant | 1 | NM_017847.6 | P1 | |||
ODR4 | ENST00000367470.8 | c.931+2015C>T | intron_variant | 5 | |||||
ODR4 | ENST00000419367.8 | c.904+2015C>T | intron_variant | 2 | |||||
ODR4 | ENST00000478571.1 | n.113+2015C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
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31
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248516Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134926
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GnomAD4 exome AF: 0.00000346 AC: 5AN: 1443802Hom.: 0 Cov.: 29 AF XY: 0.00000139 AC XY: 1AN XY: 717168
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GnomAD4 genome Cov.: 31
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2022 | The c.14C>T (p.P5L) alteration is located in exon 1 (coding exon 1) of the OCLM gene. This alteration results from a C to T substitution at nucleotide position 14, causing the proline (P) at amino acid position 5 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
N;N;N;N;N
Sift4G
Pathogenic
D
Polyphen
B
Vest4
MVP
MPC
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at