chr1-158607377-A-T

Variant names:

• chr1-158607377-A-T
• rs2427808
• NM_001004478.2:c.939A>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001004478.2(OR10Z1):​c.939A>T​(p.Gly313Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 1,609,288 control chromosomes in the GnomAD database, including 12,861 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 0.10 (875 hom., cov: 32)
  • Exomes 𝑓: 0.12 (11986 hom.)
• Consequence: OR10Z1 NM_001004478.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 11 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BP7: Synonymous conserved (PhyloP=-0.006 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004478.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10Z1	NM_001004478.2	MANE Select	c.939A>T	p.Gly313Gly	synonymous	Exon 2 of 2	NP_001004478.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR10Z1	ENST00000641002.1	MANE Select	c.939A>T	p.Gly313Gly	synonymous	Exon 2 of 2	ENSP00000493003.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15788 AN: 152072 Hom.: 871 Cov.: 32

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0707

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.105

GnomAD2 exomes AF: 0.120 AC: 29754 AN: 248258 AF XY: 0.126

Gnomad AFR exome AF: 0.0670

Gnomad AMR exome AF: 0.0993

Gnomad ASJ exome AF: 0.0728

Gnomad EAS exome AF: 0.0872

Gnomad FIN exome AF: 0.0686

Gnomad NFE exome AF: 0.130

Gnomad OTH exome AF: 0.114

GnomAD4 exome AF: 0.125 AC: 181836 AN: 1457098 Hom.: 11986 Cov.: 30 AF XY: 0.128 AC XY: 92638 AN XY: 724870

African (AFR) AF: 0.0651 AC: 2172 AN: 33376

American (AMR) AF: 0.0993 AC: 4431 AN: 44604

Ashkenazi Jewish (ASJ) AF: 0.0719 AC: 1866 AN: 25948

East Asian (EAS) AF: 0.118 AC: 4681 AN: 39668

South Asian (SAS) AF: 0.206 AC: 17707 AN: 85992

European-Finnish (FIN) AF: 0.0738 AC: 3924 AN: 53204

Middle Eastern (MID) AF: 0.120 AC: 689 AN: 5740

European-Non Finnish (NFE) AF: 0.126 AC: 139296 AN: 1108360

Other (OTH) AF: 0.117 AC: 7070 AN: 60206

GnomAD4 genome AF: 0.104 AC: 15802 AN: 152190 Hom.: 875 Cov.: 32 AF XY: 0.103 AC XY: 7630 AN XY: 74400

African (AFR) AF: 0.0642 AC: 2666 AN: 41542

American (AMR) AF: 0.112 AC: 1705 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3470

East Asian (EAS) AF: 0.0893 AC: 461 AN: 5164

South Asian (SAS) AF: 0.200 AC: 965 AN: 4820

European-Finnish (FIN) AF: 0.0707 AC: 749 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8612 AN: 67994

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.113 Hom.: 338

Bravo AF: 0.102

Asia WGS AF: 0.137 AC: 477 AN: 3478

EpiCase AF: 0.123

EpiControl AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.4
DANN	Benign	0.67
PhyloP100		-0.0060
Mutation Taster		=97/3	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2427808; hg19: chr1-158577167; COSMIC: COSV63524599; COSMIC: COSV63524599;