rs202103799

Variant names:

• chr19-14799806-C-A
• NM_001370485.4:c.331G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-14799806-C-A
• chr19-14799806-C-T

Variant summary

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

The NM_001370485.4(OR7C1):​c.331G>T​(p.Asp111Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. D111N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: OR7C1 NM_001370485.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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 rank	MANE	Protein	UniProt
OR7C1	NM_001370485.4	c.331G>T	p.Asp111Tyr	missense_variant	Exon 5 of 5	ENST00000641666.2	NP_001357414.2
OR7C1	NM_198944.1	c.331G>T	p.Asp111Tyr	missense_variant	Exon 1 of 1		NP_945182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7C1	ENST00000641666.2	c.331G>T	p.Asp111Tyr	missense_variant	Exon 5 of 5		NM_001370485.4	ENSP00000493429.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.32
BayesDel_addAF	Benign	-0.17	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Uncertain	0.97
DEOGEN2	Benign	0.0076	T;T;T;T
Eigen	Benign	-0.052
Eigen_PC	Benign	-0.39
FATHMM_MKL	Benign	0.035	N
LIST_S2	Uncertain	0.86	.;.;.;D
M_CAP	Benign	0.0017	T
MetaRNN	Uncertain	0.44	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.1	M;M;M;M
PrimateAI	Benign	0.20	T
PROVEAN	Pathogenic	-8.2	.;.;.;D
REVEL	Benign	0.085
Sift	Pathogenic	0.0	.;.;.;D
Sift4G	Pathogenic	0.0	.;.;.;D
Polyphen		1.0	D;D;D;D
Vest4		0.28
MutPred		0.62		Gain of glycosylation at T116 (P = 0.1519);Gain of glycosylation at T116 (P = 0.1519);Gain of glycosylation at T116 (P = 0.1519);Gain of glycosylation at T116 (P = 0.1519);
MVP		0.34
MPC		0.89
ClinPred		1.0	D
GERP RS		1.3
Varity_R		0.88
gMVP		0.58

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-14910618;