rs7108052

Positions:

• chr11-59475503-G-A

Variant summary

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

The NM_001004705.2(OR4D10):​c.-169+1710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 152,232 control chromosomes in the GnomAD database, including 65,880 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 0.93 (65880 hom., cov: 31)
• Consequence: OR4D10 NM_001004705.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

Genes affected

OR4D10 (HGNC:15173): (olfactory receptor family 4 subfamily D member 10) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4D10	NM_001004705.2	c.-169+1710G>A		intron_variant		ENST00000530162.2	NP_001004705.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4D10	ENST00000530162.2	c.-169+1710G>A		intron_variant			NM_001004705.2	ENSP00000436424	P1

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140989 AN: 152114 Hom.: 65852 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.927 AC: 141072 AN: 152232 Hom.: 65880 Cov.: 31 AF XY: 0.927 AC XY: 68964 AN XY: 74430

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.921

Alfa AF: 0.952 Hom.: 17735

Bravo AF: 0.911

Asia WGS AF: 0.935 AC: 3252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7108052; hg19: chr11-59242976;