rs10500600

Variant names:

• chr11-4419253-G-A
• rs10500600
• ENST00000641797.5:n.386+25088G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-4419253-G-A
• chr11-4419253-G-T

Variant summary

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

The ENST00000641797.5(ENSG00000291144):​n.386+25088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0613 in 152,100 control chromosomes in the GnomAD database, including 356 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 0.061 (356 hom., cov: 32)
• Consequence: ENSG00000291144 ENST00000641797.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 4 publications found

Genes affected

ENSG00000291144 (HGNC:):

OR51R1P (HGNC:15203): (olfactory receptor family 51 subfamily R member 1 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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291144	ENST00000641797.5		n.386+25088G>A		intron	N/A
	ENSG00000291144	ENST00000685350.2		n.391+25088G>A		intron	N/A
	ENSG00000291144	ENST00000688083.3		n.383+25088G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0613 AC: 9313 AN: 151982 Hom.: 352 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0613 AC: 9331 AN: 152100 Hom.: 356 Cov.: 32 AF XY: 0.0606 AC XY: 4501 AN XY: 74322

African (AFR) AF: 0.0519 AC: 2153 AN: 41494

American (AMR) AF: 0.111 AC: 1696 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.0561 AC: 270 AN: 4814

European-Finnish (FIN) AF: 0.0448 AC: 473 AN: 10566

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.0645 AC: 4388 AN: 67984

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0628 Hom.: 751

Bravo AF: 0.0661

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.46
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10500600; hg19: chr11-4440483;