rs11590865

Variant names:

• chr1-247998492-A-G
• rs11590865
• NM_001304535.3:c.-19+61108A>G

Variant summary

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

The NM_001304535.3(OR2L13):​c.-19+61108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0873 in 152,094 control chromosomes in the GnomAD database, including 744 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 0.087 (744 hom., cov: 32)
• Consequence: OR2L13 NM_001304535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 3 publications found

Genes affected

OR2L13 (HGNC:19578): (olfactory receptor family 2 subfamily L member 13) 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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2L13	NM_001304535.3	c.-19+61108A>G		intron_variant	Intron 1 of 1		NP_001291464.1
OR2L13	NM_175911.5	c.-144+61108A>G		intron_variant	Intron 1 of 2		NP_787107.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13257 AN: 151976 Hom.: 741 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0873 AC: 13273 AN: 152094 Hom.: 744 Cov.: 32 AF XY: 0.0850 AC XY: 6323 AN XY: 74368

African (AFR) AF: 0.160 AC: 6617 AN: 41482

American (AMR) AF: 0.0531 AC: 811 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3468

East Asian (EAS) AF: 0.157 AC: 809 AN: 5168

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4818

European-Finnish (FIN) AF: 0.0298 AC: 316 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0596 AC: 4047 AN: 67950

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0696 Hom.: 313

Bravo AF: 0.0922

Asia WGS AF: 0.0970 AC: 336 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	0.75
DANN	Benign	0.23
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11590865; hg19: chr1-248161794;