rs149900

Variant names:

• chr6-28046819-C-T
• rs149900
• ENST00000429302.1:n.386C>T

Variant summary

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

The ENST00000429302.1(OR2B7P):​n.386C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.239 in 163,212 control chromosomes in the GnomAD database, including 5,298 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 0.25 (5264 hom., cov: 31)
  • Exomes 𝑓: 0.072 (34 hom.)
• Consequence: OR2B7P ENST00000429302.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.96

Genes affected

OR2B7P (HGNC:13967): (olfactory receptor family 2 subfamily B member 7 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]

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B7P		n.28046819C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR2B7P	ENST00000429302.1	n.386C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
ZSCAN16-AS1	ENST00000660873.1	n.188+13559G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38104 AN: 151848 Hom.: 5254 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.0722 AC: 812 AN: 11246 Hom.: 34 Cov.: 0 AF XY: 0.0767 AC XY: 408 AN XY: 5320

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.0952

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0556

Gnomad4 SAS exome AF: 0.0455

Gnomad4 FIN exome AF: 0.0700

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.0942

GnomAD4 genome AF: 0.251 AC: 38147 AN: 151966 Hom.: 5264 Cov.: 31 AF XY: 0.244 AC XY: 18093 AN XY: 74272

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.239

Alfa AF: 0.220 Hom.: 5035

Bravo AF: 0.267

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	4.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149900; hg19: chr6-28014597;