rs16932816

Variant names:

• chr9-35991107-C-T
• rs16932816
• ENST00000647905.1:n.273-21930C>T

Variant summary

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

The ENST00000647905.1(ENSG00000290538):​n.273-21930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,170 control chromosomes in the GnomAD database, including 1,835 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 0.15 (1835 hom., cov: 33)
• Consequence: ENSG00000290538 ENST00000647905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

Genes affected

ENSG00000290538 (HGNC:):

OR13C6P (HGNC:15101): (olfactory receptor family 13 subfamily C member 6 pseudogene) 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290538	ENST00000647905.1	n.273-21930C>T		intron_variant	Intron 2 of 2
OR13C6P	ENST00000433495.1	n.*229G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22849 AN: 152052 Hom.: 1835 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.136

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22849 AN: 152170 Hom.: 1835 Cov.: 33 AF XY: 0.153 AC XY: 11377 AN XY: 74394

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.134

Alfa AF: 0.139 Hom.: 1346

Bravo AF: 0.144

Asia WGS AF: 0.137 AC: 479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16932816; hg19: chr9-35991104;