chr14-20229441-T-G

Variant names:

• chr14-20229441-T-G
• rs12434822
• ENST00000553765.2:c.40T>G

Variant summary

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

The ENST00000553765.2(OR11H7):​c.40T>G​(p.Leu14Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 650,184 control chromosomes in the GnomAD database, including 46,902 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.31 (8991 hom., cov: 32)
  • Exomes 𝑓: 0.38 (37911 hom.)
• Consequence: OR11H7 ENST00000553765.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 4 publications found

Genes affected

OR11H7 (HGNC:15350): (olfactory receptor family 11 subfamily H member 7 (gene/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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jan 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553765.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR11H7	NR_145509.1		n.461T>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR11H7	ENST00000553765.2	TSL:6	c.40T>G	p.Leu14Val	missense	Exon 1 of 1	ENSP00000451021.2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47369 AN: 151948 Hom.: 8993 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.342

GnomAD2 exomes AF: 0.365 AC: 34606 AN: 94720 AF XY: 0.374

Gnomad AFR exome AF: 0.0752

Gnomad AMR exome AF: 0.349

Gnomad ASJ exome AF: 0.353

Gnomad EAS exome AF: 0.355

Gnomad FIN exome AF: 0.390

Gnomad NFE exome AF: 0.419

Gnomad OTH exome AF: 0.380

GnomAD4 exome AF: 0.383 AC: 191014 AN: 498118 Hom.: 37911 Cov.: 0 AF XY: 0.386 AC XY: 102678 AN XY: 266254

African (AFR) AF: 0.0879 AC: 1247 AN: 14186

American (AMR) AF: 0.352 AC: 9860 AN: 28012

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 5736 AN: 16226

East Asian (EAS) AF: 0.307 AC: 9729 AN: 31730

South Asian (SAS) AF: 0.370 AC: 19230 AN: 51982

European-Finnish (FIN) AF: 0.390 AC: 12389 AN: 31776

Middle Eastern (MID) AF: 0.361 AC: 1369 AN: 3790

European-Non Finnish (NFE) AF: 0.414 AC: 120817 AN: 291960

Other (OTH) AF: 0.374 AC: 10637 AN: 28456

GnomAD4 genome AF: 0.311 AC: 47349 AN: 152066 Hom.: 8991 Cov.: 32 AF XY: 0.314 AC XY: 23304 AN XY: 74334

African (AFR) AF: 0.0869 AC: 3605 AN: 41502

American (AMR) AF: 0.366 AC: 5579 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1745 AN: 5178

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4810

European-Finnish (FIN) AF: 0.391 AC: 4133 AN: 10574

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28317 AN: 67962

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.373 Hom.: 25096

Bravo AF: 0.297

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Uncertain	0.99
PhyloP100		-1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12434822; hg19: chr14-20697600; COSMIC: COSV59644721;