NM_001004312.2:c.165-1169G>T

Variant names:

• chr3-187700180-C-A
• rs2017908
• NM_001004312.2:c.165-1169G>T

Variant summary

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

The NM_001004312.2(RTP2):​c.165-1169G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,146 control chromosomes in the GnomAD database, including 3,323 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 0.18 (3323 hom., cov: 33)
• Consequence: RTP2 NM_001004312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 5 publications found

Genes affected

RTP2 (HGNC:32486): (receptor transporter protein 2) Enables olfactory receptor binding activity. Involved in protein insertion into membrane. Located in cell surface. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RTP2	NM_001004312.2	c.165-1169G>T		intron_variant	Intron 1 of 1	ENST00000358241.1	NP_001004312.2
RTP2	XM_017006301.2	c.165-1169G>T		intron_variant	Intron 4 of 4		XP_016861790.1
RTP2	XM_017006302.2	c.165-1169G>T		intron_variant	Intron 4 of 4		XP_016861791.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTP2	ENST00000358241.1	c.165-1169G>T		intron_variant	Intron 1 of 1	1	NM_001004312.2	ENSP00000350976.1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27310 AN: 152028 Hom.: 3321 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.180 AC: 27334 AN: 152146 Hom.: 3323 Cov.: 33 AF XY: 0.173 AC XY: 12883 AN XY: 74384

African (AFR) AF: 0.345 AC: 14332 AN: 41512

American (AMR) AF: 0.128 AC: 1952 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3472

East Asian (EAS) AF: 0.0705 AC: 365 AN: 5180

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4824

European-Finnish (FIN) AF: 0.0759 AC: 805 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8683 AN: 67942

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.171 Hom.: 273

Bravo AF: 0.192

Asia WGS AF: 0.104 AC: 361 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	3.2
DANN	Benign	0.67
PhyloP100		-0.11
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: rs2017908; hg19: chr3-187417968;