rs9633905

Variant names:

• chr11-4475383-C-A
• rs9633905
• ENST00000531655.1:n.571C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-4475383-C-A
• chr11-4475383-C-T

Variant summary

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

The ENST00000641797.5(ENSG00000291144):​n.1185C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 1,547,232 control chromosomes in the GnomAD database, including 71,605 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 0.26 (5647 hom., cov: 33)
  • Exomes 𝑓: 0.30 (65958 hom.)
• Consequence: ENSG00000291144 ENST00000641797.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 5 publications found

Genes affected

OR52K3P (HGNC:15224): (olfactory receptor family 52 subfamily K member 3 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]

ENSG00000291144 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641797.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR52K3P	ENST00000531655.1	TSL:6	n.571C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000291144	ENST00000641797.5		n.1185C>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000291144	ENST00000690343.2		n.1020C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39516 AN: 152018 Hom.: 5637 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.269

GnomAD4 exome AF: 0.305 AC: 425011 AN: 1395096 Hom.: 65958 Cov.: 27 AF XY: 0.303 AC XY: 211625 AN XY: 697792

African (AFR) AF: 0.130 AC: 4193 AN: 32152

American (AMR) AF: 0.322 AC: 14358 AN: 44546

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 5767 AN: 25626

East Asian (EAS) AF: 0.348 AC: 13711 AN: 39372

South Asian (SAS) AF: 0.259 AC: 21979 AN: 84714

European-Finnish (FIN) AF: 0.385 AC: 20523 AN: 53352

Middle Eastern (MID) AF: 0.214 AC: 1212 AN: 5654

European-Non Finnish (NFE) AF: 0.310 AC: 326459 AN: 1051570

Other (OTH) AF: 0.289 AC: 16809 AN: 58110

GnomAD4 genome AF: 0.260 AC: 39539 AN: 152136 Hom.: 5647 Cov.: 33 AF XY: 0.263 AC XY: 19543 AN XY: 74356

African (AFR) AF: 0.142 AC: 5884 AN: 41522

American (AMR) AF: 0.278 AC: 4245 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 796 AN: 3466

East Asian (EAS) AF: 0.366 AC: 1891 AN: 5166

South Asian (SAS) AF: 0.247 AC: 1192 AN: 4818

European-Finnish (FIN) AF: 0.390 AC: 4120 AN: 10576

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20488 AN: 67982

Other (OTH) AF: 0.268 AC: 567 AN: 2114

Alfa AF: 0.270 Hom.: 1133

Bravo AF: 0.251

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.3
DANN	Benign	0.73
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs9633905; hg19: chr11-4496613;