rs11130094

Variant names:

• chr3-46500013-G-A
• rs11130094
• NM_031440.2:c.156-343G>A

Variant summary

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

The NM_031440.2(RTP3):​c.156-343G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,152 control chromosomes in the GnomAD database, including 8,659 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 0.31 (8659 hom., cov: 32)
• Consequence: RTP3 NM_031440.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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
RTP3	NM_031440.2	c.156-343G>A		intron_variant	Intron 1 of 1	ENST00000296142.4	NP_113628.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTP3	ENST00000296142.4	c.156-343G>A		intron_variant	Intron 1 of 1	1	NM_031440.2	ENSP00000296142.3
RTP3	ENST00000684260.1	c.156-343G>A		intron_variant	Intron 2 of 2			ENSP00000507138.1

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46491 AN: 152034 Hom.: 8652 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.306 AC: 46498 AN: 152152 Hom.: 8659 Cov.: 32 AF XY: 0.311 AC XY: 23135 AN XY: 74362

Gnomad4 AFR AF: 0.0845

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.294

Alfa AF: 0.349 Hom.: 1728

Bravo AF: 0.293

Asia WGS AF: 0.425 AC: 1476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.28

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: rs11130094; hg19: chr3-46541503;