rs10500600

Variant names:

• chr11-4419253-G-A
• rs10500600
• ENST00000641797.4:n.383+25088G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000641797.4(ENSG00000291144):​n.383+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 ENST00000641797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

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

Verdict is Benign. Variant got -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.

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
ENSG00000291144	ENST00000641797.4	n.383+25088G>A		intron_variant	Intron 1 of 2
ENSG00000291144	ENST00000685350.1	n.363+25088G>A		intron_variant	Intron 1 of 2
ENSG00000291144	ENST00000688083.2	n.378+25088G>A		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.0519

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.0645

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0610 Hom.: 477

Bravo AF: 0.0661

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500600; hg19: chr11-4440483;