11-124568716-C-T

Variant names:

• chr11-124568716-C-T
• rs10893268
• ENST00000641670.1:c.-19-1385C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641670.1. 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
	OR8A1	ENST00000641670.1		c.-19-1385C>T		intron	N/A	ENSP00000492950.1	A0A286YEW5

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

African (AFR) AF: 0.479 AC: 19840 AN: 41436

American (AMR) AF: 0.382 AC: 5839 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4816

European-Finnish (FIN) AF: 0.319 AC: 3362 AN: 10550

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24262 AN: 67948

Other (OTH) AF: 0.374 AC: 790 AN: 2112

Alfa AF: 0.384 Hom.: 4785

Bravo AF: 0.410

Asia WGS AF: 0.448 AC: 1557 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10893268; hg19: chr11-124438612;