chr1-158808974-T-G

Position:

• chr1-158808974-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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]

OR6N1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR6N1	XM_017000325.2	c.-194+31341A>C		intron_variant			XP_016855814.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR10AA1P	ENST00000417823.1	n.362A>C		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.339

Gnomad4 NFE exome AF: 0.243

Gnomad4 OTH exome AF: 0.293

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

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.316

Alfa AF: 0.280 Hom.: 8914

Bravo AF: 0.348

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7550055; hg19: chr1-158778764;