3-46499657-T-C

Variant names:

• chr3-46499657-T-C
• rs7430431
• NM_031440.2:c.156-699T>C

Variant summary

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

The NM_031440.2(RTP3):​c.156-699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,084 control chromosomes in the GnomAD database, including 30,716 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 0.62 (30716 hom., cov: 32)
• Consequence: RTP3 NM_031440.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RTP3	NM_031440.2	c.156-699T>C		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.156-699T>C		intron_variant	Intron 1 of 1	1	NM_031440.2	ENSP00000296142.3
RTP3	ENST00000684260.1	c.156-699T>C		intron_variant	Intron 2 of 2			ENSP00000507138.1

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94762 AN: 151966 Hom.: 30657 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.624 AC: 94888 AN: 152084 Hom.: 30716 Cov.: 32 AF XY: 0.634 AC XY: 47157 AN XY: 74354

African (AFR) AF: 0.743 AC: 30811 AN: 41484

American (AMR) AF: 0.618 AC: 9444 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3470

East Asian (EAS) AF: 0.965 AC: 4986 AN: 5166

South Asian (SAS) AF: 0.738 AC: 3554 AN: 4816

European-Finnish (FIN) AF: 0.634 AC: 6724 AN: 10604

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35514 AN: 67952

Other (OTH) AF: 0.562 AC: 1189 AN: 2114

Alfa AF: 0.551 Hom.: 99295

Bravo AF: 0.626

Asia WGS AF: 0.831 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.76
PhyloP100		-0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7430431; hg19: chr3-46541147;