rs10415312

Positions:

• chr19-14799626-C-A
• chr19-14799626-C-G
• chr19-14799626-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001370485.4(OR7C1):​c.511G>T​(p.Glu171Ter) variant causes a stop gained 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: OR7C1 NM_001370485.4 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.03

Genes affected

OR7C1 (HGNC:8373): (olfactory receptor family 7 subfamily C 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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR7C1	NM_001370485.4	c.511G>T	p.Glu171Ter	stop_gained	5/5	ENST00000641666.2	NP_001357414.2
OR7C1	NM_198944.1	c.511G>T	p.Glu171Ter	stop_gained	1/1		NP_945182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR7C1	ENST00000641666.2	c.511G>T	p.Glu171Ter	stop_gained	5/5		NM_001370485.4	ENSP00000493429	P1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 78

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.0027	T
BayesDel_noAF	Benign	-0.24
CADD	Pathogenic	26
DANN	Benign	0.87
Eigen	Benign	-0.81
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0042	N
MutationTaster	Benign	6.1e-8	P
Vest4		0.016
GERP RS		-7.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10415312; hg19: chr19-14910438;