chr11-56381651-C-T

Variant names:

• chr11-56381651-C-T
• rs1945245
• ENST00000534005.1:n.17C>T

Variant summary

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

The ENST00000534005.1(OR8L1P):​n.17C>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 0.247 in 151,904 control chromosomes in the GnomAD database, including 4,740 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 0.25 (4740 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: OR8L1P ENST00000534005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85
• Publications: 2 publications found

Genes affected

OR8L1P (HGNC:15316): (olfactory receptor family 8 subfamily L 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR8L1P		n.56381651C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR8L1P	ENST00000534005.1	n.17C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37544 AN: 151782 Hom.: 4739 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.247 AC: 37555 AN: 151900 Hom.: 4740 Cov.: 32 AF XY: 0.241 AC XY: 17927 AN XY: 74256

African (AFR) AF: 0.255 AC: 10572 AN: 41444

American (AMR) AF: 0.187 AC: 2859 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3472

East Asian (EAS) AF: 0.135 AC: 696 AN: 5168

South Asian (SAS) AF: 0.193 AC: 929 AN: 4814

European-Finnish (FIN) AF: 0.194 AC: 2046 AN: 10570

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.270 AC: 18298 AN: 67870

Other (OTH) AF: 0.245 AC: 516 AN: 2108

Alfa AF: 0.256 Hom.: 1052

Bravo AF: 0.249

Asia WGS AF: 0.152 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.28
PhyloP100		-4.9

Splicing

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

Other links and lift over

dbSNP: rs1945245; hg19: chr11-56149127;