ENST00000560066.1:n.31-32T>C

Variant names:

• chr15-101842890-T-C
• rs7169868
• ENST00000560066.1:n.31-32T>C

Variant summary

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

The ENST00000560066.1(OR4F13P):​n.31-32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,874 control chromosomes in the GnomAD database, including 17,266 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 0.47 (17266 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: OR4F13P ENST00000560066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR4F13P	NR_046417.1	n.31-32T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR4F13P	ENST00000560066.1	n.31-32T>C		intron_variant	Intron 1 of 4	6

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71158 AN: 151756 Hom.: 17257 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.465

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.469 AC: 71199 AN: 151874 Hom.: 17266 Cov.: 31 AF XY: 0.459 AC XY: 34070 AN XY: 74220

African (AFR) AF: 0.518 AC: 21471 AN: 41412

American (AMR) AF: 0.432 AC: 6593 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3468

East Asian (EAS) AF: 0.0575 AC: 297 AN: 5162

South Asian (SAS) AF: 0.424 AC: 2038 AN: 4806

European-Finnish (FIN) AF: 0.359 AC: 3774 AN: 10522

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.498 AC: 33864 AN: 67936

Other (OTH) AF: 0.464 AC: 979 AN: 2108

Alfa AF: 0.482 Hom.: 13177

Bravo AF: 0.468

Asia WGS AF: 0.324 AC: 1127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.7
DANN	Benign	0.87
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs7169868; hg19: chr15-102383093;