19-110949-C-G

Position:

• chr19-110949-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001005240.3(OR4F17):​c.271C>G​(p.Leu91Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 25)
  • Exomes 𝑓: 0.0000019 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: OR4F17 NM_001005240.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -4.06

Genes affected

OR4F17 (HGNC:15381): (olfactory receptor family 4 subfamily F member 17) 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]

OR4F17 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05918327).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4F17	NM_001005240.3	c.271C>G	p.Leu91Val	missense_variant	3/3	ENST00000585993.3	NP_001005240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4F17	ENST00000585993.3	c.271C>G	p.Leu91Val	missense_variant	3/3	6	NM_001005240.3	ENSP00000467301.1
OR4F17	ENST00000618231.3	c.334C>G	p.Leu112Val	missense_variant	2/2	6		ENSP00000493422.2
OR4F17	ENST00000318050.4	c.271C>G	p.Leu91Val	missense_variant	1/1	6		ENSP00000315047.3
OR4F17	ENST00000641591.1	n.194+268C>G		intron_variant

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000187 AC: 2 AN: 1070622 Hom.: 0 Cov.: 16 AF XY: 0.00000183 AC XY: 1 AN XY: 545446

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000494

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 25

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 03, 2022

The c.271C>G (p.L91V) alteration is located in exon 1 (coding exon 1) of the OR4F17 gene. This alteration results from a C to G substitution at nucleotide position 271, causing the leucine (L) at amino acid position 91 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.2
DANN	Benign	0.91
DEOGEN2	Benign	0.0050	T;.;T
Eigen	Benign	-0.97
Eigen_PC	Benign	-0.95
FATHMM_MKL	Benign	0.057	N
LIST_S2	Benign	0.76	.;T;T
M_CAP	Benign	0.00054	T
MetaRNN	Benign	0.059	T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.63	N;.;N
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-0.070	.;.;N
REVEL	Benign	0.013
Sift	Benign	0.36	.;.;T
Sift4G	Benign	0.22	T;.;T
Polyphen		0.088	B;.;B
Vest4		0.14
MutPred		0.34		Loss of catalytic residue at L91 (P = 0.071);.;Loss of catalytic residue at L91 (P = 0.071);
MVP		0.40
MPC		2.1
ClinPred		0.050	T
GERP RS		0.13
Varity_R		0.068
gMVP		0.019

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411902561; hg19: chr19-110949;