rs637249

Variant names:

• chr11-56480601-A-C
• rs637249
• ENST00000641241.1:n.67-139T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-56480601-A-C
• chr11-56480601-A-T

Variant summary

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

The ENST00000641241.1(ENSG00000290753):​n.67-139T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,254 control chromosomes in the GnomAD database, including 1,165 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 0.12 (1165 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000290753 ENST00000641241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 0 publications found

Genes affected

ENSG00000290753 (HGNC:):

OR5M2P (HGNC:14803): (olfactory receptor family 5 subfamily M member 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 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
ENSG00000290753	ENST00000641241.1	n.67-139T>G		intron_variant	Intron 1 of 1
OR5M2P	ENST00000529003.1	n.-174T>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18001 AN: 152134 Hom.: 1165 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.118 AC: 18005 AN: 152254 Hom.: 1165 Cov.: 33 AF XY: 0.122 AC XY: 9053 AN XY: 74424

African (AFR) AF: 0.104 AC: 4315 AN: 41566

American (AMR) AF: 0.0979 AC: 1498 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3470

East Asian (EAS) AF: 0.144 AC: 746 AN: 5184

South Asian (SAS) AF: 0.119 AC: 573 AN: 4822

European-Finnish (FIN) AF: 0.198 AC: 2096 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8149 AN: 68010

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.0769 Hom.: 116

Bravo AF: 0.111

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.50
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs637249; hg19: chr11-56248077;