rs1902318

Positions:

• chr11-5002909-G-A

Variant summary

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

The NM_001004755.2(OR51L1):​c.*2979G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,990 control chromosomes in the GnomAD database, including 6,633 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 0.29 (6632 hom., cov: 31)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: OR51L1 NM_001004755.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

OR51L1 (HGNC:14759): (olfactory receptor family 51 subfamily L member 1) 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR51L1	NM_001004755.2	c.*2979G>A		3_prime_UTR_variant	3/3	ENST00000641819.1	NP_001004755.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR51L1	ENST00000641819.1	c.*2979G>A		3_prime_UTR_variant	3/3		NM_001004755.2	ENSP00000493015	P1
OR51L1	ENST00000641624.1	n.926G>A		non_coding_transcript_exon_variant	3/4
OR51L1	ENST00000642056.1	n.926G>A		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43841 AN: 151854 Hom.: 6628 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.289 AC: 43871 AN: 151976 Hom.: 6632 Cov.: 31 AF XY: 0.285 AC XY: 21178 AN XY: 74276

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.273

Alfa AF: 0.295 Hom.: 3227

Bravo AF: 0.286

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902318; hg19: chr11-5024139;