NM_001001958.1:c.928T>C

Variant names:

• chr19-9126023-A-G
• rs780595264
• NM_001001958.1:c.928T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001001958.1(OR7G3):​c.928T>C​(p.Ser310Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000792 in 1,502,796 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000073 (0 hom.)
• Consequence: OR7G3 NM_001001958.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.211
• Publications: 1 publications found

Genes affected

OR7G3 (HGNC:8467): (olfactory receptor family 7 subfamily G member 3) 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.007301897).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001958.1. 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
	OR7G3	NM_001001958.1	MANE Select	c.928T>C	p.Ser310Pro	missense	Exon 1 of 1	NP_001001958.1	Q8NG95

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7G3	ENST00000305444.2	TSL:6 MANE Select	c.928T>C	p.Ser310Pro	missense	Exon 1 of 1	ENSP00000302867.2	Q8NG95

Frequencies

GnomAD3 genomes AF: 0.000224 AC: 13 AN: 58132 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000125

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000307

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000261 AC: 30 AN: 114856 AF XY: 0.000272

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00588

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000559

Gnomad OTH exome AF: 0.000354

GnomAD4 exome AF: 0.0000734 AC: 106 AN: 1444664 Hom.: 0 Cov.: 32 AF XY: 0.0000824 AC XY: 59 AN XY: 716362

African (AFR) AF: 0.00 AC: 0 AN: 33096

American (AMR) AF: 0.00 AC: 0 AN: 43730

Ashkenazi Jewish (ASJ) AF: 0.00308 AC: 78 AN: 25354

East Asian (EAS) AF: 0.00 AC: 0 AN: 39358

South Asian (SAS) AF: 0.00 AC: 0 AN: 85170

European-Finnish (FIN) AF: 0.0000188 AC: 1 AN: 53128

Middle Eastern (MID) AF: 0.000395 AC: 2 AN: 5062

European-Non Finnish (NFE) AF: 0.00000727 AC: 8 AN: 1100186

Other (OTH) AF: 0.000285 AC: 17 AN: 59580

GnomAD4 genome AF: 0.000224 AC: 13 AN: 58132 Hom.: 0 Cov.: 0 AF XY: 0.000174 AC XY: 5 AN XY: 28774

African (AFR) AF: 0.00 AC: 0 AN: 4834

American (AMR) AF: 0.000125 AC: 1 AN: 8026

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 11 AN: 1660

East Asian (EAS) AF: 0.00 AC: 0 AN: 2256

South Asian (SAS) AF: 0.00 AC: 0 AN: 2194

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4870

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 178

European-Non Finnish (NFE) AF: 0.0000307 AC: 1 AN: 32528

Other (OTH) AF: 0.00 AC: 0 AN: 898

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000756

ExAC AF: 0.0000942 AC: 10

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.7
DANN	Benign	0.89
DEOGEN2	Benign	0.0048	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.0042	N
LIST_S2	Benign	0.26	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.0073	T
MetaSVM	Benign	-0.93	T
MutationAssessor	Benign	0.97	L
PhyloP100		-0.21
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.014
Sift	Benign	0.051	T
Sift4G	Uncertain	0.047	D
Polyphen		0.011	B
Vest4		0.086
MutPred		0.34		Loss of MoRF binding (P = 0.0224)
MVP		0.15
MPC		0.11
ClinPred		0.016	T
GERP RS		-0.63
Varity_R		0.21
gMVP		0.087
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs780595264; hg19: chr19-9236699;