rs10497907

chr2-208626029-C-A

Variant summary

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

The NR_136588.1(LOC101927960):n.506-30797C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 151,678 control chromosomes in the GnomAD database, including 792 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 0.066 (792 hom., cov: 32)
• Consequence: LOC101927960 NR_136588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84

Genes affected

LOC101927960 (HGNC:):

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927960	NR_136588.1	n.506-30797C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTH2R	ENST00000419079.1	c.*99-30797C>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0658 AC: 9969 AN: 151560 Hom.: 796 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.00954

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.0666

Gnomad FIN AF: 0.00462

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0658 AC: 9979 AN: 151678 Hom.: 792 Cov.: 32 AF XY: 0.0647 AC XY: 4795 AN XY: 74146

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.00954

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.0660

Gnomad4 FIN AF: 0.00462

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0470

Alfa AF: 0.0434 Hom.: 65

Bravo AF: 0.0725

Asia WGS AF: 0.0570 AC: 199 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.049
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497907; hg19: chr2-209490753;