1-247954114-T-G

Variant names:

• chr1-247954114-T-G
• rs10888287
• NM_001304535.3:c.-19+16730T>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+16730T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,084 control chromosomes in the GnomAD database, including 56,861 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 0.84 (56861 hom., cov: 31)
• Consequence: OR2L13 NM_001304535.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2L13	NM_001304535.3	c.-19+16730T>G		intron_variant	Intron 1 of 1		NP_001291464.1
OR2L13	NM_175911.5	c.-144+16730T>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: 0.837 AC: 127149 AN: 151966 Hom.: 56849 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.836 AC: 127207 AN: 152084 Hom.: 56861 Cov.: 31 AF XY: 0.841 AC XY: 62548 AN XY: 74352

African (AFR) AF: 0.482 AC: 19950 AN: 41432

American (AMR) AF: 0.935 AC: 14284 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3230 AN: 3472

East Asian (EAS) AF: 0.911 AC: 4721 AN: 5180

South Asian (SAS) AF: 0.971 AC: 4676 AN: 4816

European-Finnish (FIN) AF: 0.993 AC: 10531 AN: 10602

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66869 AN: 67998

Other (OTH) AF: 0.879 AC: 1849 AN: 2104

Alfa AF: 0.944 Hom.: 262189

Bravo AF: 0.815

Asia WGS AF: 0.910 AC: 3166 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	3.1
DANN	Benign	0.57
PhyloP100		0.0070
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10888287; hg19: chr1-248117416;