chr17-3062708-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_014566.1(OR1D5):​c.900G>A​(p.Pro300=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,587,880 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.00031 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00019 ( 0 hom. )

Consequence

OR1D5
NM_014566.1 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.981
Variant links:
Genes affected
OR1D5 (HGNC:8186): (olfactory receptor family 1 subfamily D member 5) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-3062708-C-T is Benign according to our data. Variant chr17-3062708-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647228.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.981 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR1D5NM_014566.1 linkuse as main transcriptc.900G>A p.Pro300= synonymous_variant 1/1 ENST00000575751.1 NP_055381.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR1D5ENST00000575751.1 linkuse as main transcriptc.900G>A p.Pro300= synonymous_variant 1/1 NM_014566.1 ENSP00000459028 P1

Frequencies

GnomAD3 genomes
AF:
0.000310
AC:
47
AN:
151598
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000581
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000656
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000201
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000177
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000103
AC:
25
AN:
241566
Hom.:
0
AF XY:
0.000122
AC XY:
16
AN XY:
131552
show subpopulations
Gnomad AFR exome
AF:
0.000272
Gnomad AMR exome
AF:
0.000118
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000157
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000186
AC:
267
AN:
1436166
Hom.:
0
Cov.:
29
AF XY:
0.000182
AC XY:
130
AN XY:
715842
show subpopulations
Gnomad4 AFR exome
AF:
0.000212
Gnomad4 AMR exome
AF:
0.000134
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000254
Gnomad4 SAS exome
AF:
0.0000467
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000222
Gnomad4 OTH exome
AF:
0.0000841
GnomAD4 genome
AF:
0.000310
AC:
47
AN:
151714
Hom.:
0
Cov.:
31
AF XY:
0.000270
AC XY:
20
AN XY:
74094
show subpopulations
Gnomad4 AFR
AF:
0.000580
Gnomad4 AMR
AF:
0.000655
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000202
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000177
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000253
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJul 01, 2022OR1D5: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
10
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs369254607; hg19: chr17-2966002; COSMIC: COSV101643452; API