11-58506897-T-C

Variant names:

• chr11-58506897-T-C
• rs2515366
• NM_001005218.3:c.*279A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000360374.3(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 ENST00000360374.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887
• Publications: 3 publications found

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]

ENSG00000255299 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000360374.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5B21	NM_001005218.3	MANE Select	c.*279A>G		3_prime_UTR	Exon 1 of 1	NP_001005218.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5B21	ENST00000360374.3	TSL:6 MANE Select	c.*279A>G		3_prime_UTR	Exon 1 of 1	ENSP00000353537.2
	ENSG00000255299	ENST00000754072.1		n.518-1355A>G		intron	N/A

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

African (AFR) AF: 0.350 AC: 14496 AN: 41446

American (AMR) AF: 0.573 AC: 8758 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3468

East Asian (EAS) AF: 0.703 AC: 3634 AN: 5166

South Asian (SAS) AF: 0.546 AC: 2631 AN: 4820

European-Finnish (FIN) AF: 0.491 AC: 5170 AN: 10536

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39642 AN: 67978

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.558 Hom.: 58002

Bravo AF: 0.517

Asia WGS AF: 0.602 AC: 2095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.89

Splicing

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

Other links and lift over

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