rs10497907

Variant names:

• chr2-208626029-C-A
• rs10497907
• ENST00000419079.1:n.*99-30797C>A

Variant summary

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

The ENST00000419079.1(PTH2R):​n.*99-30797C>A variant causes a intron 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: PTH2R ENST00000419079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 3 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]

LOC101927960 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC101927960	NR_136588.1	n.506-30797C>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000419079.1	n.*99-30797C>A		intron_variant	Intron 3 of 6	2		ENSP00000393930.1

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

African (AFR) AF: 0.190 AC: 7890 AN: 41436

American (AMR) AF: 0.0285 AC: 433 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.00954 AC: 33 AN: 3460

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5184

South Asian (SAS) AF: 0.0660 AC: 318 AN: 4818

European-Finnish (FIN) AF: 0.00462 AC: 49 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1000 AN: 67672

Other (OTH) AF: 0.0470 AC: 99 AN: 2108

Alfa AF: 0.0388 Hom.: 114

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs10497907; hg19: chr2-209490753;