X-131619414-A-G

Variant names:

• chrX-131619414-A-G
• rs10521771
• ENST00000454899.2:n.402A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454899.2(OR2AF1P):​n.402A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 110,158 control chromosomes in the GnomAD database, including 5,557 homozygotes. There are 11,361 hemizygotes in GnomAD. 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 0.36 (5555 hom., 11357 hem., cov: 22)
  • Exomes 𝑓: 0.80 (2 hom. 4 hem.)
• Consequence: OR2AF1P ENST00000454899.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 0 publications found

Genes affected

OR2AF1P (HGNC:14719): (olfactory receptor family 2 subfamily AF 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]

ENSG00000286060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2AF1P		n.131619414A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2AF1P	ENST00000454899.2	n.402A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286060	ENST00000836463.1	n.1327A>G		non_coding_transcript_exon_variant	Exon 7 of 7
ENSG00000286060	ENST00000836464.1	n.*9A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.361 AC: 39763 AN: 110092 Hom.: 5560 Cov.: 22

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.476

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.354

GnomAD4 exome AF: 0.800 AC: 8 AN: 10 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.800 AC: 8 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.361 AC: 39756 AN: 110148 Hom.: 5555 Cov.: 22 AF XY: 0.350 AC XY: 11357 AN XY: 32488

African (AFR) AF: 0.230 AC: 6991 AN: 30415

American (AMR) AF: 0.336 AC: 3463 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1498 AN: 2616

East Asian (EAS) AF: 0.397 AC: 1369 AN: 3447

South Asian (SAS) AF: 0.419 AC: 1070 AN: 2553

European-Finnish (FIN) AF: 0.380 AC: 2190 AN: 5756

Middle Eastern (MID) AF: 0.467 AC: 99 AN: 212

European-Non Finnish (NFE) AF: 0.422 AC: 22206 AN: 52649

Other (OTH) AF: 0.350 AC: 525 AN: 1502

Alfa AF: 0.404 Hom.: 50002

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.012
DANN	Benign	0.47
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10521771; hg19: chrX-130753416;