rs145155372

Variant names:

• chr3-98264652-C-G
• rs145155372
• NM_001005479.2:c.320C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-98264652-C-G
• chr3-98264652-C-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001005479.2(OR5H6):​c.320C>G​(p.Thr107Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000057 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR5H6 NM_001005479.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0200
• Publications: 0 publications found

Genes affected

OR5H6 (HGNC:14767): (olfactory receptor family 5 subfamily H member 6) 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jul 2015]

ENSG00000251088 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.048126817).
• BP6: Variant 3-98264652-C-G is Benign according to our data. Variant chr3-98264652-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2305560.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005479.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5H6	NM_001005479.2	MANE Select	c.320C>G	p.Thr107Ser	missense	Exon 1 of 1	NP_001005479.2	A0A126GW86

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR5H6	ENST00000615035.3	TSL:6 MANE Select	c.320C>G	p.Thr107Ser	missense	Exon 1 of 1	ENSP00000480705.3	A0A126GW86
	ENSG00000251088	ENST00000508616.1	TSL:1	n.26+30976C>G		intron	N/A
	OR5H6	ENST00000642105.1		c.368C>G	p.Thr123Ser	missense	Exon 1 of 1	ENSP00000493340.1	Q8NGV6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 53646 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00 AC: 0 AN: 248586 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000566 AC: 2 AN: 353658 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 177730

African (AFR) AF: 0.00 AC: 0 AN: 19500

American (AMR) AF: 0.00 AC: 0 AN: 22664

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7124

East Asian (EAS) AF: 0.00 AC: 0 AN: 33228

South Asian (SAS) AF: 0.00 AC: 0 AN: 32208

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12362

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1524

European-Non Finnish (NFE) AF: 0.00000958 AC: 2 AN: 208808

Other (OTH) AF: 0.00 AC: 0 AN: 16240

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 53646 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 26460

African (AFR) AF: 0.00 AC: 0 AN: 23504

American (AMR) AF: 0.00 AC: 0 AN: 5874

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 924

East Asian (EAS) AF: 0.00 AC: 0 AN: 4112

South Asian (SAS) AF: 0.00 AC: 0 AN: 1818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2598

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 100

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13856

Other (OTH) AF: 0.00 AC: 0 AN: 674

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ExAC AF: 0.0000351 AC: 3

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.43	T
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.17
DANN	Benign	0.55
DEOGEN2	Benign	0.0017	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0059	N
LIST_S2	Benign	0.0053	T
M_CAP	Benign	0.00030	T
MetaRNN	Benign	0.048	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.77	N
PhyloP100		0.020
PrimateAI	Benign	0.18	T
Polyphen		0.0	B
MutPred		0.30		Loss of glycosylation at T123 (P = 0.148)
ClinPred		0.069	T
GERP RS		-0.20
PromoterAI		-0.00060	Neutral
Varity_R		0.045
gMVP		0.067
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs145155372; hg19: chr3-97983496;