rs4910907

Variant names:

• chr11-4147621-G-A
• rs4910907
• ENST00000641518.1:n.1093C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-4147621-G-A
• chr11-4147621-G-T

Variant summary

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

The ENST00000641518.1(OR55B1P):​n.1093C>T 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 0.886 in 152,228 control chromosomes in the GnomAD database, including 59,949 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 0.89 (59948 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: OR55B1P ENST00000641518.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

Genes affected

OR55B1P (HGNC:15241): (olfactory receptor family 55 subfamily B 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.925 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
OR55B1P	ENST00000641518.1	n.1093C>T		non_coding_transcript_exon_variant	Exon 2 of 2
OR55B1P	ENST00000641245.1	n.51-284C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134757 AN: 152106 Hom.: 59942 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.884

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.886 AC: 134804 AN: 152224 Hom.: 59948 Cov.: 33 AF XY: 0.881 AC XY: 65576 AN XY: 74414

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.931

Gnomad4 OTH AF: 0.877

Alfa AF: 0.920 Hom.: 29333

Bravo AF: 0.877

Asia WGS AF: 0.789 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4910907; hg19: chr11-4168851;