3-46496528-G-T

Variant names:

• chr3-46496528-G-T
• rs883739
• ENST00000684260.1:c.-702-833G>T

Variant summary

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

The ENST00000684260.1(RTP3):​c.-702-833G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,032 control chromosomes in the GnomAD database, including 10,608 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 0.37 (10608 hom., cov: 32)
• Consequence: RTP3 ENST00000684260.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 15 publications found

Genes affected

RTP3 (HGNC:15572): (receptor transporter protein 3) Predicted to enable olfactory receptor binding activity. Involved in detection of chemical stimulus involved in sensory perception of bitter taste and protein targeting to membrane. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTP3	ENST00000684260.1	c.-702-833G>T		intron_variant	Intron 1 of 2			ENSP00000507138.1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56251 AN: 151914 Hom.: 10600 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.370 AC: 56280 AN: 152032 Hom.: 10608 Cov.: 32 AF XY: 0.373 AC XY: 27705 AN XY: 74286

African (AFR) AF: 0.311 AC: 12895 AN: 41442

American (AMR) AF: 0.385 AC: 5887 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1616 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2497 AN: 5186

South Asian (SAS) AF: 0.391 AC: 1882 AN: 4816

European-Finnish (FIN) AF: 0.423 AC: 4458 AN: 10548

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25898 AN: 67962

Other (OTH) AF: 0.343 AC: 724 AN: 2110

Alfa AF: 0.311 Hom.: 1200

Bravo AF: 0.368

Asia WGS AF: 0.424 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.14
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs883739; hg19: chr3-46538018;