chr15-101844841-T-C

Variant names:

• chr15-101844841-T-C
• rs1513981
• ENST00000560066.1:n.211+1268T>C

Variant summary

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

The ENST00000560066.1(OR4F13P):​n.211+1268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,132 control chromosomes in the GnomAD database, including 36,536 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 0.68 (36536 hom., cov: 32)
• Consequence: OR4F13P ENST00000560066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 3 publications found

Genes affected

OR4F13P (HGNC:):

OR4F13P (HGNC:15076): (olfactory receptor family 4 subfamily F member 13 pseudogene) 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR4F13P	NR_046417.1	n.211+1268T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4F13P	ENST00000560066.1	n.211+1268T>C		intron_variant	Intron 3 of 4	6

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102953 AN: 152014 Hom.: 36486 Cov.: 32

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.677 AC: 103050 AN: 152132 Hom.: 36536 Cov.: 32 AF XY: 0.668 AC XY: 49645 AN XY: 74362

African (AFR) AF: 0.869 AC: 36076 AN: 41538

American (AMR) AF: 0.565 AC: 8638 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2108 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5172

South Asian (SAS) AF: 0.686 AC: 3304 AN: 4818

European-Finnish (FIN) AF: 0.510 AC: 5396 AN: 10572

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44096 AN: 67964

Other (OTH) AF: 0.645 AC: 1363 AN: 2114

Alfa AF: 0.653 Hom.: 55414

Bravo AF: 0.679

Asia WGS AF: 0.499 AC: 1736 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.6
DANN	Benign	0.55
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1513981; hg19: chr15-102385044;