Genetic Variant OR7D2:p.Pro25Gln (chr19-9185855-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_175883.4(OR7D2):c.74C>A(p.Pro25Gln) variant causes a missense 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. 14/21 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. P25L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

OR7D2
NM_175883.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.728

Publications

4 publications found

Variant links:

Genes affected

OR7D2 (HGNC:8378): (olfactory receptor family 7 subfamily D member 2) 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]

OR7D2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.17967686).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175883.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7D2	NM_175883.4	MANE Select	c.74C>A	p.Pro25Gln	missense	Exon 3 of 3	NP_787079.1	Q96RA2
	OR7D2	NM_001386112.1		c.74C>A	p.Pro25Gln	missense	Exon 2 of 2	NP_001373041.1	Q96RA2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
OR7D2	ENST00000641288.2	MANE Select	c.74C>A	p.Pro25Gln	missense	Exon 3 of 3	ENSP00000493200.1	Q96RA2
OR7D2	ENST00000344248.4	TSL:6	c.74C>A	p.Pro25Gln	missense	Exon 1 of 1	ENSP00000345563.2	Q96RA2
OR7D2	ENST00000642043.1		c.74C>A	p.Pro25Gln	missense	Exon 2 of 2	ENSP00000492939.1	Q96RA2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1460606

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

726594

African (AFR)

AF:

0.00

AC:

AN:

33454

American (AMR)

AF:

0.00

AC:

AN:

44674

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25984

East Asian (EAS)

AF:

0.00

AC:

AN:

39694

South Asian (SAS)

AF:

0.00

AC:

AN:

86034

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53310

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5752

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1111366

Other (OTH)

AF:

0.00

AC:

AN:

60338

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.18

Eigen

Benign

-0.16

Eigen_PC

Benign

-0.44

FATHMM_MKL

Benign

0.063

LIST_S2

Benign

0.40

M_CAP

Benign

0.0010

MetaRNN

Benign

0.18

MetaSVM

Benign

-0.84

MutationAssessor

Benign

1.2

PhyloP100

-0.73

PrimateAI

Benign

0.20

PROVEAN

Uncertain

-4.2

REVEL

Benign

0.060

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.038

Polyphen

1.0

Vest4

0.23

MutPred

0.34

Loss of catalytic residue at P25 (P = 0.0728)

MVP

0.55

MPC

0.17

ClinPred

0.89

GERP RS

2.2

PromoterAI

-0.014

Neutral

(source)

Varity_R

0.10

Mutation Taster

=96/4

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over