19-14886209-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000641113.1(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 ENST00000641113.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641113.1. 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
	OR7A17	NM_030901.2	MANE Select	c.-563A>G		upstream_gene	N/A	NP_112163.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7A17	ENST00000641113.1	MANE Select	c.-563A>G		upstream_gene	N/A	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.588 AC: 20 AN: 34

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.406 AC: 16825 AN: 41452

American (AMR) AF: 0.516 AC: 7897 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1391 AN: 3464

East Asian (EAS) AF: 0.826 AC: 4280 AN: 5184

South Asian (SAS) AF: 0.605 AC: 2914 AN: 4814

European-Finnish (FIN) AF: 0.393 AC: 4136 AN: 10518

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27898 AN: 67974

Other (OTH) AF: 0.442 AC: 935 AN: 2114

Alfa AF: 0.425 Hom.: 36421

Bravo AF: 0.443

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.64
PhyloP100		-1.4
PromoterAI		0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4808631; hg19: chr19-14997021;