chr11-58506897-T-C

Position:

• chr11-58506897-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005218.3(OR5B21):​c.*279A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,028 control chromosomes in the GnomAD database, including 20,988 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 0.51 (20988 hom., cov: 32)
• Consequence: OR5B21 NM_001005218.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

Genes affected

OR5B21 (HGNC:19616): (olfactory receptor family 5 subfamily B member 21) 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]

LOC105369313 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR5B21	NM_001005218.3	c.*279A>G		3_prime_UTR_variant	1/1	ENST00000360374.3	NP_001005218.1
LOC105369313	XR_007062673.1	n.239-1355A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR5B21	ENST00000360374.3	c.*279A>G		3_prime_UTR_variant	1/1	6	NM_001005218.3	ENSP00000353537.2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78157 AN: 151910 Hom.: 20978 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.530

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.514 AC: 78194 AN: 152028 Hom.: 20988 Cov.: 32 AF XY: 0.513 AC XY: 38119 AN XY: 74282

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.532

Alfa AF: 0.575 Hom.: 39788

Bravo AF: 0.517

Asia WGS AF: 0.602 AC: 2095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2515366; hg19: chr11-58274370; COSMIC: COSV64482089;