rs10497899

chr2-208383522-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PTH2R	NM_001309516.2	c.-259+23285A>T		intron_variant
PTH2R	NM_001371905.1	c.-326+23285A>T		intron_variant
PTH2R	NM_001371906.1	c.-335+23285A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTH2R	ENST00000617735.4	c.-259+23285A>T		intron_variant		2

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

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.0664

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.0189

Gnomad4 OTH AF: 0.0572

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497899; hg19: chr2-209248247;