Variant rs8109935 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001005191.3(OR7D4):c.651C>T(p.Ser217Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 1,613,186 control chromosomes in the GnomAD database, including 10,447 homozygotes. 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: 𝑓 0.15 ( 2773 hom., cov: 31)

Exomes 𝑓: 0.089 ( 7674 hom. )

Consequence

OR7D4
NM_001005191.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.246

Variant links:

Genes affected

OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D member 4) 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]

OR7D4 links:

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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]

OR7E24 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR7D4	NM_001005191.3 link	c.651C>T	p.Ser217Ser	synonymous_variant	2/2	ENST00000641669.1	NP_001005191.1	Q8NG98A0A126GVR1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
OR7D4	ENST00000641669.1 link	c.651C>T	p.Ser217Ser	synonymous_variant	2/2		NM_001005191.3	ENSP00000493383.1	Q8NG98
OR7D4	ENST00000308682.3 link	c.651C>T	p.Ser217Ser	synonymous_variant	1/1	6		ENSP00000310488.2	Q8NG98
OR7D4	ENST00000641244.1 link	c.651C>T	p.Ser217Ser	synonymous_variant	2/2			ENSP00000493404.1	Q8NG98

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22728

AN:

151974

Hom.:

2766

Cov.:

show subpopulations

Gnomad AFR

AF:

0.324

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.128

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0504

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.0269

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.0746

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.109

AC:

27439

AN:

251330

Hom.:

2228

AF XY:

0.110

AC XY:

14926

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.332

Gnomad AMR exome

AF:

0.118

Gnomad ASJ exome

AF:

0.105

Gnomad EAS exome

AF:

0.0543

Gnomad SAS exome

AF:

0.197

Gnomad FIN exome

AF:

0.0285

Gnomad NFE exome

AF:

0.0763

Gnomad OTH exome

AF:

0.0985

GnomAD4 exome

AF:

0.0892

AC:

130318

AN:

1461094

Hom.:

7674

Cov.:

AF XY:

0.0925

AC XY:

67206

AN XY:

726884

show subpopulations

Gnomad4 AFR exome

AF:

0.335

Gnomad4 AMR exome

AF:

0.120

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.0423

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.0298

Gnomad4 NFE exome

AF:

0.0746

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.150

AC:

22763

AN:

152092

Hom.:

2773

Cov.:

AF XY:

0.148

AC XY:

10994

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.324

Gnomad4 AMR

AF:

0.128

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.0505

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0269

Gnomad4 NFE

AF:

0.0746

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.110

Hom.:

812

Bravo

AF:

0.164

Asia WGS

AF:

0.129

AC:

451

AN:

3478

EpiCase

AF:

0.0864

EpiControl

AF:

0.0869

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

8.0

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.16

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over