rs11603357

Positions:

• chr11-4431820-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000527287.1(OR52P2P):​n.458G>A 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 0.0564 in 153,044 control chromosomes in the GnomAD database, including 326 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 0.057 (326 hom., cov: 33)
  • Exomes 𝑓: 0.038 (0 hom.)
• Consequence: OR52P2P ENST00000527287.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

Genes affected

OR52P2P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR52P2P		n.4431820C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR52P2P	ENST00000527287.1	n.458G>A		non_coding_transcript_exon_variant	1/1	6
ENSG00000291144	ENST00000641797.4	n.384-37547C>T		intron_variant
ENSG00000291144	ENST00000685350.1	n.364-37547C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 8590 AN: 152182 Hom.: 324 Cov.: 33

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0567

Gnomad FIN AF: 0.0446

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0512

GnomAD4 exome AF: 0.0375 AC: 28 AN: 746 Hom.: 0 Cov.: 0 AF XY: 0.0378 AC XY: 17 AN XY: 450

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0383

Gnomad4 NFE exome AF: 0.0316

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0565 AC: 8606 AN: 152298 Hom.: 326 Cov.: 33 AF XY: 0.0564 AC XY: 4199 AN XY: 74466

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0565

Gnomad4 FIN AF: 0.0446

Gnomad4 NFE AF: 0.0640

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0681 Hom.: 81

Bravo AF: 0.0602

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603357; hg19: chr11-4453050;