dbSNP rs1325773250: OR13D1:p.Ala300Thr (chr9-104695415-G-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001004484.2(OR13D1):c.898G>A(p.Ala300Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000698 in 1,431,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A300S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 7.0e-7 ( 0 hom. )

Consequence

OR13D1
NM_001004484.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.652

Publications

0 publications found

Variant links:

Genes affected

OR13D1 (HGNC:14695): (olfactory receptor family 13 subfamily D member 1) 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]

OR13D1 links:

ENSG00000297079 (HGNC:):

ENSG00000297079 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.37046435).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR13D1	NM_001004484.2 link	c.898G>A	p.Ala300Thr	missense_variant	Exon 1 of 1	ENST00000641530.1	NP_001004484.2	Q8NGV5
LOC107987105	XR_007061705.1 link	n.192-4208C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR13D1	ENST00000641530.1 link	c.898G>A	p.Ala300Thr	missense_variant	Exon 1 of 1		NM_001004484.2	ENSP00000493337.1		A0A286YF94

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.98e-7

AC:

AN:

1431992

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

711134

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

31694

American (AMR)

AF:

0.00

AC:

AN:

36588

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24194

East Asian (EAS)

AF:

0.00

AC:

AN:

39502

South Asian (SAS)

AF:

0.00

AC:

AN:

80560

European-Finnish (FIN)

AF:

0.0000190

AC:

AN:

52584

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5570

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1102326

Other (OTH)

AF:

0.00

AC:

AN:

58974

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Benign

-0.50

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.012

T;.

Eigen

Benign

-0.056

Eigen_PC

Benign

-0.26

FATHMM_MKL

Benign

0.24

LIST_S2

Uncertain

0.89

D;D

M_CAP

Benign

0.014

MetaRNN

Benign

0.37

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.1

M;.

PhyloP100

0.65

PrimateAI

Benign

0.19

PROVEAN

Uncertain

-3.3

D;.

REVEL

Benign

0.093

Sift

Uncertain

0.0090

D;.

Sift4G

Pathogenic

0.0010

D;.

Polyphen

0.99

D;.

Vest4

0.37

MutPred

0.65

Loss of MoRF binding (P = 0.1308);.;

MVP

0.12

MPC

0.12

ClinPred

0.94

GERP RS

3.9

Varity_R

0.25

gMVP

0.19

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over