GeneBe

NM_007346.4:c.972C>T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_007346.4(OGFR):​c.972C>T​(p.Ser324Ser) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OGFR
NM_007346.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.967

Publications

1 publications found
Variant links:
Genes affected
OGFR (HGNC:15768): (opioid growth factor receptor) The protein encoded by this gene is a receptor for opioid growth factor (OGF), also known as [Met(5)]-enkephalin. OGF is a negative regulator of cell proliferation and tissue organization in a variety of processes. The encoded unbound receptor for OGF has been localized to the outer nuclear envelope, where it binds OGF and is translocated into the nucleus. The coding sequence of this gene contains a polymorphic region of 60 nt tandem imperfect repeat units. Several transcripts containing between zero and eight repeat units have been reported. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP7
Synonymous conserved (PhyloP=-0.967 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OGFRNM_007346.4 linkc.972C>T p.Ser324Ser synonymous_variant Exon 7 of 7 ENST00000290291.10 NP_031372.2 Q9NZT2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OGFRENST00000290291.10 linkc.972C>T p.Ser324Ser synonymous_variant Exon 7 of 7 1 NM_007346.4 ENSP00000290291.6 Q9NZT2-1
OGFRENST00000370461.5 linkc.816C>T p.Ser272Ser synonymous_variant Exon 5 of 5 2 ENSP00000359491.1 A0A0A0MRN5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
173470
AF XY:
0.00
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 FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1419302
Hom.:
0
Cov.:
71
AF XY:
0.00
AC XY:
0
AN XY:
702300
African (AFR)
AF:
0.00
AC:
0
AN:
32534
American (AMR)
AF:
0.00
AC:
0
AN:
37750
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25458
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37532
South Asian (SAS)
AF:
0.00
AC:
0
AN:
81512
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49042
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5706
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1090918
Other (OTH)
AF:
0.00
AC:
0
AN:
58850
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
1.7
DANN
Benign
0.84
PhyloP100
-0.97
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Other links and lift over

dbSNP: rs756096081; hg19: chr20-61443939; API