chr1-247452638-C-T

Position:

• chr1-247452638-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001004492.2(OR2B11):​c.-656G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00858 in 154,066 control chromosomes in the GnomAD database, including 11 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 0.0086 (11 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (0 hom.)
• Consequence: OR2B11 NM_001004492.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

Genes affected

OR2B11 (HGNC:31249): (olfactory receptor family 2 subfamily B member 11) 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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2B11	NM_001004492.2	c.-656G>A		5_prime_UTR_variant	2/2	ENST00000641149.2	NP_001004492.1
OR2B11	NR_169840.1	n.483-197G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B11	ENST00000641149.2	c.-656G>A		5_prime_UTR_variant	2/2		NM_001004492.2	ENSP00000492892	P1
OR2B11	ENST00000641527.1	c.-656G>A		5_prime_UTR_variant	3/3			ENSP00000493421	P1
OR2B11	ENST00000641613.1	n.483-197G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00861 AC: 1311 AN: 152190 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00278

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.00813

GnomAD4 exome AF: 0.00626 AC: 11 AN: 1758 Hom.: 0 Cov.: 0 AF XY: 0.00313 AC XY: 3 AN XY: 960

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00408

Gnomad4 NFE exome AF: 0.00966

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00861 AC: 1311 AN: 152308 Hom.: 11 Cov.: 32 AF XY: 0.00771 AC XY: 574 AN XY: 74476

Gnomad4 AFR AF: 0.00277

Gnomad4 AMR AF: 0.0102

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.0145

Gnomad4 OTH AF: 0.00805

Alfa AF: 0.0121 Hom.: 2

Bravo AF: 0.00875

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72655366; hg19: chr1-247615940;