1-158605939-C-T

Variant names:

• chr1-158605939-C-T
• rs857684
• NM_001004478.2:c.-113-387C>T

Variant summary

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

The NM_001004478.2(OR10Z1):​c.-113-387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,994 control chromosomes in the GnomAD database, including 4,914 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 0.24 (4914 hom., cov: 32)
• Consequence: OR10Z1 NM_001004478.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 24 publications found

Genes affected

OR10Z1 (HGNC:14996): (olfactory receptor family 10 subfamily Z member 1) 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR10Z1	NM_001004478.2	c.-113-387C>T		intron_variant	Intron 1 of 1	ENST00000641002.1	NP_001004478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR10Z1	ENST00000641002.1	c.-113-387C>T		intron_variant	Intron 1 of 1		NM_001004478.2	ENSP00000493003.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37082 AN: 151874 Hom.: 4906 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.244 AC: 37127 AN: 151994 Hom.: 4914 Cov.: 32 AF XY: 0.249 AC XY: 18528 AN XY: 74270

African (AFR) AF: 0.159 AC: 6595 AN: 41470

American (AMR) AF: 0.307 AC: 4684 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3468

East Asian (EAS) AF: 0.494 AC: 2541 AN: 5148

South Asian (SAS) AF: 0.182 AC: 875 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3468 AN: 10536

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17204 AN: 67974

Other (OTH) AF: 0.262 AC: 552 AN: 2106

Alfa AF: 0.239 Hom.: 3054

Bravo AF: 0.245

Asia WGS AF: 0.360 AC: 1250 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	0.037
DANN	Benign	0.69
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs857684; hg19: chr1-158575729;