rs4435030

Positions:

• chr11-75094960-C-A
• chr11-75094960-C-G
• chr11-75094960-C-T

Variant summary

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

The NM_001005285.2(OR2AT4):​c.-652+1864G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,032 control chromosomes in the GnomAD database, including 24,792 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 0.53 (24792 hom., cov: 31)
• Consequence: OR2AT4 NM_001005285.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

Genes affected

OR2AT4 (HGNC:19620): (olfactory receptor family 2 subfamily AT member 4) 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]

ENSG00000284722 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR2AT4	NM_001005285.2	c.-652+1864G>T		intron_variant			NP_001005285.1
OR2AT4	NM_001405852.1	c.-652+1868G>T		intron_variant			NP_001392781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2AT4	ENST00000641504.1	c.-652+1868G>T		intron_variant				ENSP00000493318.1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81053 AN: 151914 Hom.: 24740 Cov.: 31

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.534 AC: 81171 AN: 152032 Hom.: 24792 Cov.: 31 AF XY: 0.534 AC XY: 39647 AN XY: 74288

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.476

Alfa AF: 0.396 Hom.: 16567

Bravo AF: 0.560

Asia WGS AF: 0.645 AC: 2240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4435030; hg19: chr11-74806005;