11-124568716-C-T

Position:

• chr11-124568716-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641670.1(OR8A1):​c.-19-1385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,962 control chromosomes in the GnomAD database, including 12,428 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 0.40 (12428 hom., cov: 32)
• Consequence: OR8A1 ENST00000641670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.847

Genes affected

OR8A1 (HGNC:8469): (olfactory receptor family 8 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR8A1	ENST00000641670.1	c.-19-1385C>T		intron_variant				ENSP00000492950	P1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60309 AN: 151842 Hom.: 12422 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.374

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.397 AC: 60366 AN: 151962 Hom.: 12428 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74284

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.374

Alfa AF: 0.377 Hom.: 2695

Bravo AF: 0.410

Asia WGS AF: 0.448 AC: 1557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.23
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10893268; hg19: chr11-124438612;