rs1339562141

Variant names:

• chr7-144259246-G-A
• rs1339562141
• NM_001005328.2:c.383C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-144259246-G-A
• chr7-144259246-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3

The NM_001005328.2(OR2A7):​c.383C>T​(p.Pro128Leu) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. 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. P128H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 17)
• Consequence: OR2A7 NM_001005328.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.80

Genes affected

OR2A7 (HGNC:8234): (olfactory receptor family 2 subfamily A member 7) 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]

ARHGEF34P (HGNC:38086): (Rho guanine nucleotide exchange factor 34, pseudogene)

ARHGEF35-AS1 (HGNC:41292): (ARHGEF35 antisense RNA 1)

ENSG00000284644 (HGNC:):

OR2A1-AS1 (HGNC:49168): (OR2A1 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.811

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2A7	NM_001005328.2	c.383C>T	p.Pro128Leu	missense_variant	Exon 2 of 2	ENST00000641841.1	NP_001005328.1
ARHGEF34P	NR_033942.1	n.3954C>T		non_coding_transcript_exon_variant	Exon 13 of 13
ARHGEF35-AS1	NR_126022.1	n.494-21226G>A		intron_variant	Intron 2 of 4
OR2A1-AS1	NR_126023.1	n.608-19503C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2A7	ENST00000641841.1	c.383C>T	p.Pro128Leu	missense_variant	Exon 2 of 2		NM_001005328.2	ENSP00000493320.1

Frequencies

GnomAD3 genomes Cov.: 17

GnomAD4 exome Cov.: 11

GnomAD4 genome Cov.: 17

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.035	T
BayesDel_noAF	Benign	-0.29
CADD	Uncertain	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.087	T;T
Eigen	Uncertain	0.46
Eigen_PC	Benign	0.21
FATHMM_MKL	Pathogenic	0.98	D
M_CAP	Benign	0.034	D
MetaRNN	Pathogenic	0.81	D;D
MetaSVM	Benign	-1.2	T
MutationAssessor	Pathogenic	3.1	M;M
PrimateAI	Benign	0.32	T
PROVEAN	Pathogenic	-9.8	.;D
REVEL	Benign	0.19
Sift	Pathogenic	0.0	.;D
Sift4G	Pathogenic	0.0	.;D
Polyphen		1.0	D;D
Vest4		0.91
MutPred		0.62		Gain of MoRF binding (P = 0.1039);Gain of MoRF binding (P = 0.1039);
MVP		0.59
ClinPred		1.0	D
GERP RS		2.1
Varity_R		0.52
gMVP		0.37

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

LitVar

Other links and lift over

dbSNP: rs1339562141; hg19: chr7-143956339;