6-29553512-C-T

Variant names:

• chr6-29553512-C-T
• NM_001396058.1:c.294C>T
• OR2I1 p.Ala98Ala

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001396058.1(OR2I1):​c.294C>T​(p.Ala98Ala) variant causes a synonymous 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR2I1 NM_001396058.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.60
• Publications: 0 publications found

Genes affected

OR2I1 (HGNC:8258): (olfactory receptor family 2 subfamily I member 1 pseudogene) 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 -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP7: Synonymous conserved (PhyloP=-4.6 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001396058.1. 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
	OR2I1	NM_001396058.1	MANE Select	c.294C>T	p.Ala98Ala	synonymous	Exon 2 of 2	NP_001382987.1	Q8NGU4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2I1	ENST00000641137.2	MANE Select	c.294C>T	p.Ala98Ala	synonymous	Exon 2 of 2	ENSP00000493715.1	Q8NGU4
	OR2I1	ENST00000641730.1		n.1156C>T		non_coding_transcript_exon	Exon 2 of 2
	OR2I1	ENST00000642037.1		n.482C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 246298 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 124904

African (AFR) AF: 0.00 AC: 0 AN: 7162

American (AMR) AF: 0.00 AC: 0 AN: 7426

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9222

East Asian (EAS) AF: 0.00 AC: 0 AN: 22892

South Asian (SAS) AF: 0.00 AC: 0 AN: 3032

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20850

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1298

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 158058

Other (OTH) AF: 0.00 AC: 0 AN: 16358

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.9
DANN	Benign	0.94
PhyloP100		-4.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-29521289;