rs8109935

chr19-9214187-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005191.3(OR7D4):c.651C>T(p.Ser217=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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]

OR7E24 (HGNC:):

ACMG classification

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	UniProt
OR7D4	NM_001005191.3	c.651C>T	p.Ser217=	synonymous_variant	2/2	ENST00000641669.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR7D4	ENST00000641669.1	c.651C>T	p.Ser217=	synonymous_variant	2/2		NM_001005191.3	P1
OR7D4	ENST00000308682.3	c.651C>T	p.Ser217=	synonymous_variant	1/1			P1
OR7D4	ENST00000641244.1	c.651C>T	p.Ser217=	synonymous_variant	2/2			P1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22728 AN: 151974 Hom.: 2766 Cov.: 31

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

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.: 33 AF XY: 0.0925 AC XY: 67206 AN XY: 726884

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.: 31 AF XY: 0.148 AC XY: 10994 AN XY: 74354

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

Other links and lift over

dbSNP: rs8109935; hg19: chr19-9324863; COSMIC: COSV58071723; COSMIC: COSV58071723;