rs1368988913

Variant names:

• chr8-166172-C-A
• rs1368988913
• NM_001005504.1:c.853G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-166172-C-A
• chr8-166172-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001005504.1(OR4F21):​c.853G>T​(p.Val285Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V285I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000088 (0 hom., cov: 2)
  • Exomes 𝑓: 0.0000037 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR4F21 NM_001005504.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

Genes affected

OR4F21 (HGNC:19583): (olfactory receptor family 4 subfamily F member 21) 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]

ENSG00000292979 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.14222959).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005504.1. 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
	OR4F21	NM_001005504.1	MANE Select	c.853G>T	p.Val285Phe	missense	Exon 1 of 1	NP_001005504.1	O95013

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR4F21	ENST00000320901.4	TSL:6 MANE Select	c.853G>T	p.Val285Phe	missense	Exon 1 of 1	ENSP00000318878.3	O95013
	ENSG00000292979	ENST00000805562.1		n.115+65957G>T		intron	N/A
	ENSG00000292979	ENST00000805563.1		n.136+66804G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000884 AC: 1 AN: 11314 Hom.: 0 Cov.: 2

Gnomad AFR AF: 0.000165

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

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000365 AC: 1 AN: 273602 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 146876

African (AFR) AF: 0.00 AC: 0 AN: 10534

American (AMR) AF: 0.00 AC: 0 AN: 11388

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8084

East Asian (EAS) AF: 0.00 AC: 0 AN: 14920

South Asian (SAS) AF: 0.00 AC: 0 AN: 29954

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16868

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1138

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 165100

Other (OTH) AF: 0.0000640 AC: 1 AN: 15616

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000884 AC: 1 AN: 11314 Hom.: 0 Cov.: 2 AF XY: 0.000189 AC XY: 1 AN XY: 5282

African (AFR) AF: 0.000165 AC: 1 AN: 6072

American (AMR) AF: 0.00 AC: 0 AN: 340

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 174

East Asian (EAS) AF: 0.00 AC: 0 AN: 50

South Asian (SAS) AF: 0.00 AC: 0 AN: 70

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 12

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4064

Other (OTH) AF: 0.00 AC: 0 AN: 66

Alfa AF: 0.000169 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Uncertain	0.98
DEOGEN2	Benign	0.020	T
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.60
FATHMM_MKL	Benign	0.043	N
LIST_S2	Benign	0.69	T
M_CAP	Benign	0.0012	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.83	L
PhyloP100		-1.3
PrimateAI	Benign	0.24	T
PROVEAN	Uncertain	-3.4	D
REVEL	Benign	0.14
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.048	D
Polyphen		0.20	B
Vest4		0.39
MutPred		0.39		Loss of MoRF binding (P = 0.1739)
MVP		0.15
ClinPred		0.80	D
GERP RS		2.0
Varity_R		0.23
gMVP		0.15
Mutation Taster		=96/4	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.18		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: rs1368988913; hg19: chr8-116172;