1-158808974-T-G

Variant names:

• chr1-158808974-T-G
• rs7550055
• XM_017000325.2:c.-194+31341A>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000417823.1(OR10AA1P):​n.362A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.34 in 152,678 control chromosomes in the GnomAD database, including 9,597 homozygotes. 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: 𝑓 0.34 (9556 hom., cov: 30)
  • Exomes 𝑓: 0.32 (41 hom.)
• Consequence: OR10AA1P ENST00000417823.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.73
• Publications: 9 publications found

Genes affected

OR6N1 (HGNC:15034): (olfactory receptor family 6 subfamily N 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]

OR10AA1P (HGNC:14989): (olfactory receptor family 10 subfamily AA 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417823.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10AA1P	ENST00000417823.1	TSL:6	n.362A>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51637 AN: 151754 Hom.: 9523 Cov.: 30

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.309

GnomAD4 exome AF: 0.323 AC: 260 AN: 806 Hom.: 41 Cov.: 0 AF XY: 0.325 AC XY: 149 AN XY: 458

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AF: 0.500 AC: 2 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.339 AC: 185 AN: 546

Middle Eastern (MID) AF: 0.833 AC: 5 AN: 6

European-Non Finnish (NFE) AF: 0.243 AC: 36 AN: 148

Other (OTH) AF: 0.293 AC: 27 AN: 92

GnomAD4 genome AF: 0.340 AC: 51712 AN: 151872 Hom.: 9556 Cov.: 30 AF XY: 0.349 AC XY: 25911 AN XY: 74212

African (AFR) AF: 0.408 AC: 16906 AN: 41402

American (AMR) AF: 0.394 AC: 6008 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3464

East Asian (EAS) AF: 0.573 AC: 2925 AN: 5102

South Asian (SAS) AF: 0.566 AC: 2723 AN: 4808

European-Finnish (FIN) AF: 0.307 AC: 3247 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17618 AN: 67960

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.290 Hom.: 13174

Bravo AF: 0.348

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs7550055; hg19: chr1-158778764;