chrX-131619414-A-G

Position:

• chrX-131619414-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

OR2AF1P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
OR2AF1P		n.131619414A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2AF1P	ENST00000454899.2	n.402A>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.361 AC: 39763 AN: 110092 Hom.: 5560 Cov.: 22 AF XY: 0.350 AC XY: 11340 AN XY: 32422

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

Gnomad4 NFE exome AF: 0.800

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.350

Alfa AF: 0.419 Hom.: 39408

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521771; hg19: chrX-130753416;