1-186401059-C-T

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

Scores

1
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.644
Variant links:
Genes affected
ODR4 (HGNC:24299): (odr-4 GPCR localization factor homolog) Predicted to be involved in protein localization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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
ODR4NM_017847.6 linkuse as main transcriptc.1000+2015C>T intron_variant ENST00000287859.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ODR4ENST00000287859.11 linkuse as main transcriptc.1000+2015C>T intron_variant 1 NM_017847.6 P1Q5SWX8-1
ODR4ENST00000367470.8 linkuse as main transcriptc.931+2015C>T intron_variant 5 Q5SWX8-2
ODR4ENST00000419367.8 linkuse as main transcriptc.904+2015C>T intron_variant 2 Q5SWX8-4
ODR4ENST00000478571.1 linkuse as main transcriptn.113+2015C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.0000161
AC:
4
AN:
248516
Hom.:
0
AF XY:
0.0000222
AC XY:
3
AN XY:
134926
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000178
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.00000346
AC:
5
AN:
1443802
Hom.:
0
Cov.:
29
AF XY:
0.00000139
AC XY:
1
AN XY:
717168
show subpopulations
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000364
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Alfa
AF:
0.0000312
Hom.:
0
Bravo
AF:
0.00000378
ExAC
AF:
0.0000248
AC:
3

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 submitterclinical testingAmbry GeneticsNov 19, 2022The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.35
CADD
Benign
0.39
DANN
Benign
0.78
DEOGEN2
Benign
0.10
T
FATHMM_MKL
Benign
0.0080
N
M_CAP
Benign
0.0014
T
MetaRNN
Benign
0.058
T
MutationTaster
Benign
1.0
N;N;N;N;N
Sift4G
Pathogenic
0.0
D
Polyphen
0.0030
B
Vest4
0.21
MVP
0.095
MPC
0.64
GERP RS
-2.5
Varity_R
0.034
gMVP
0.13

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs757077225; hg19: chr1-186370191; API