chr6-29430002-C-T

Position:

• chr6-29430002-C-T

Variant summary

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

The NM_001394828.1(OR11A1):​c.-140+299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,066 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: OR11A1 NM_001394828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

OR11A1 (HGNC:8176): (olfactory receptor family 11 subfamily A member 1) 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]

OR5V1 (HGNC:13972): (olfactory receptor family 5 subfamily V member 1) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR11A1	NM_001394828.1	c.-140+299G>A		intron_variant		ENST00000377149.5	NP_001381757.1
OR11A1	NM_013937.4	c.-92+1862G>A		intron_variant			NP_039225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR11A1	ENST00000377149.5	c.-140+299G>A		intron_variant			NM_001394828.1	ENSP00000366354	P1
OR5V1	ENST00000377154.1	c.-197+1862G>A		intron_variant				ENSP00000366359	P1
OR11A1	ENST00000641152.2	c.-92+1862G>A		intron_variant				ENSP00000493093	P1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33253 AN: 151948 Hom.: 4094 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.219 AC: 33256 AN: 152066 Hom.: 4093 Cov.: 32 AF XY: 0.217 AC XY: 16154 AN XY: 74320

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.221

Alfa AF: 0.260 Hom.: 5363

Bravo AF: 0.207

Asia WGS AF: 0.122 AC: 426 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	0.43
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs9295805; hg19: chr6-29397779;