10-45258725-C-T

Position:

• chr10-45258725-C-T

Variant summary

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

The ENST00000436165.1(OR6D1P):​n.541C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.459 in 152,186 control chromosomes in the GnomAD database, including 17,561 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 0.46 (17531 hom., cov: 32)
  • Exomes 𝑓: 0.62 (30 hom.)
• Consequence: OR6D1P ENST00000436165.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.56

Genes affected

OR6D1P (HGNC:14849): (olfactory receptor family 6 subfamily D member 1 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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR6D1P	ENST00000436165.1	n.541C>T		non_coding_transcript_exon_variant	1/1
	ENST00000641209.1	n.333C>T		non_coding_transcript_exon_variant	2/2
	ENST00000641007.1	n.763C>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69787 AN: 151920 Hom.: 17526 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.476

GnomAD4 exome AF: 0.623 AC: 91 AN: 146 Hom.: 30 Cov.: 0 AF XY: 0.568 AC XY: 50 AN XY: 88

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.694

Gnomad4 NFE exome AF: 0.628

Gnomad4 OTH exome AF: 0.900

GnomAD4 genome AF: 0.459 AC: 69825 AN: 152040 Hom.: 17531 Cov.: 32 AF XY: 0.465 AC XY: 34596 AN XY: 74322

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.477

Alfa AF: 0.463 Hom.: 2950

Bravo AF: 0.432

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	14
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1890739; hg19: chr10-45754173;