7-144318164-C-T

Position:

• chr7-144318164-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001005287.2(OR2A1):​c.40C>T​(p.Leu14Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00075 (0 hom., cov: 17)
  • Exomes 𝑓: 0.00099 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2A1 NM_001005287.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.18

Genes affected

OR2A1 (HGNC:8229): (olfactory receptor family 2 subfamily A 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]

ENSG00000284644 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 7-144318164-C-T is Benign according to our data. Variant chr7-144318164-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2658125.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.18 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2A1	NM_001005287.2	c.40C>T	p.Leu14Leu	synonymous_variant	2/2	ENST00000641044.2	NP_001005287.1
OR2A1	XM_047420323.1	c.40C>T	p.Leu14Leu	synonymous_variant	2/2		XP_047276279.1
OR2A1-AS1	NR_126023.1	n.494-6460G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2A1	ENST00000641044.2	c.40C>T	p.Leu14Leu	synonymous_variant	2/2		NM_001005287.2	ENSP00000493454.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 99 AN: 131396 Hom.: 0 Cov.: 17 FAILED QC

Gnomad AFR AF: 0.0000590

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000317

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000517

Gnomad FIN AF: 0.00280

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00104

Gnomad OTH AF: 0.00119

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000995 AC: 592 AN: 595256 Hom.: 1 Cov.: 6 AF XY: 0.000876 AC XY: 278 AN XY: 317206

Gnomad4 AFR exome AF: 0.000188

Gnomad4 AMR exome AF: 0.000302

Gnomad4 ASJ exome AF: 0.0000514

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000188

Gnomad4 FIN exome AF: 0.00293

Gnomad4 NFE exome AF: 0.00114

Gnomad4 OTH exome AF: 0.000928

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000753 AC: 99 AN: 131496 Hom.: 0 Cov.: 17 AF XY: 0.000725 AC XY: 46 AN XY: 63462

Gnomad4 AFR AF: 0.0000588

Gnomad4 AMR AF: 0.000316

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000518

Gnomad4 FIN AF: 0.00280

Gnomad4 NFE AF: 0.00104

Gnomad4 OTH AF: 0.00117

Alfa AF: 0.00107 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

OR2A1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	5.5
DANN	Benign	0.63

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: rs753888301; hg19: chr7-144015257;