19-14886209-T-C

Variant names:

• chr19-14886209-T-C
• rs4808631
• NM_030901.2:c.-563A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030901.2(OR7A17):​c.-563A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,050 control chromosomes in the GnomAD database, including 15,362 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 0.44 (15356 hom., cov: 32)
  • Exomes 𝑓: 0.59 (6 hom.)
• Consequence: OR7A17 NM_030901.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

OR7A17 (HGNC:8363): (olfactory receptor family 7 subfamily A 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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR7A17	NM_030901.2	c.-563A>G		upstream_gene_variant		ENST00000641113.1	NP_112163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7A17	ENST00000641113.1	c.-563A>G		upstream_gene_variant			NM_030901.2	ENSP00000493283.1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66582 AN: 151898 Hom.: 15330 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.440

GnomAD4 exome AF: 0.588 AC: 20 AN: 34 Hom.: 6 AF XY: 0.625 AC XY: 15 AN XY: 24

Gnomad4 NFE exome AF: 0.588

GnomAD4 genome AF: 0.438 AC: 66656 AN: 152016 Hom.: 15356 Cov.: 32 AF XY: 0.446 AC XY: 33151 AN XY: 74284

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.442

Alfa AF: 0.423 Hom.: 23972

Bravo AF: 0.443

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4808631; hg19: chr19-14997021;