rs10497899

Variant names:

• chr2-208383522-A-T
• rs10497899
• NM_001309516.2:c.-259+23285A>T

Variant summary

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

The NM_001309516.2(PTH2R):​c.-259+23285A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,090 control chromosomes in the GnomAD database, including 625 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 0.061 (625 hom., cov: 33)
• Consequence: PTH2R NM_001309516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 5 publications found

Genes affected

PTH2R (HGNC:9609): (parathyroid hormone 2 receptor) The protein encoded by this gene is a member of the G-protein coupled receptor 2 family. This protein is a receptor for parathyroid hormone (PTH). This receptor is more selective in ligand recognition and has a more specific tissue distribution compared to parathyroid hormone receptor 1 (PTHR1). It is activated only by PTH and not by parathyroid hormone-like hormone (PTHLH) and is particularly abundant in brain and pancreas. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

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 (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTH2R	NM_001309516.2	c.-259+23285A>T		intron_variant	Intron 1 of 12		NP_001296445.1
PTH2R	NM_001371905.1	c.-326+23285A>T		intron_variant	Intron 1 of 13		NP_001358834.1
PTH2R	NM_001371906.1	c.-335+23285A>T		intron_variant	Intron 1 of 13		NP_001358835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000617735.4	c.-259+23285A>T		intron_variant	Intron 1 of 12	2		ENSP00000482485.1

Frequencies

GnomAD3 genomes AF: 0.0615 AC: 9340 AN: 151972 Hom.: 624 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0189

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0615 AC: 9352 AN: 152090 Hom.: 625 Cov.: 33 AF XY: 0.0602 AC XY: 4473 AN XY: 74364

African (AFR) AF: 0.166 AC: 6882 AN: 41444

American (AMR) AF: 0.0278 AC: 424 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.0472 AC: 244 AN: 5174

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4816

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10590

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0189 AC: 1282 AN: 67998

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0426 Hom.: 49

Bravo AF: 0.0680

Asia WGS AF: 0.0610 AC: 214 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	1.5
DANN	Benign	0.53
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs10497899; hg19: chr2-209248247;