chr6-29447687-C-A

Variant names:

• chr6-29447687-C-A
• rs2523443
• NM_001394828.1:c.-389+9300G>T

Variant summary

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

The NM_001394828.1(OR11A1):​c.-389+9300G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,264 control chromosomes in the GnomAD database, including 354 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 0.052 (354 hom., cov: 32)
• Consequence: OR11A1 NM_001394828.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 20 publications found

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]

LOC105379641 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR11A1	NM_001394828.1	c.-389+9300G>T		intron_variant	Intron 1 of 4	ENST00000377149.5	NP_001381757.1
LOC105379641	XR_002956335.1	n.81-5116G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR11A1	ENST00000377149.5	c.-389+9300G>T		intron_variant	Intron 1 of 4	6	NM_001394828.1	ENSP00000366354.1

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7978 AN: 152146 Hom.: 354 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0524 AC: 7975 AN: 152264 Hom.: 354 Cov.: 32 AF XY: 0.0467 AC XY: 3477 AN XY: 74446

African (AFR) AF: 0.0144 AC: 600 AN: 41552

American (AMR) AF: 0.0220 AC: 337 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4820

European-Finnish (FIN) AF: 0.0413 AC: 438 AN: 10602

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6331 AN: 68014

Other (OTH) AF: 0.0341 AC: 72 AN: 2114

Alfa AF: 0.0625 Hom.: 365

Bravo AF: 0.0498

Asia WGS AF: 0.00346 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.21
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2523443; hg19: chr6-29415464;