rs10497908

Variant names:

• chr2-208643567-C-T
• rs10497908
• ENST00000419079.1:n.*99-13259C>T

Variant summary

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

The ENST00000419079.1(PTH2R):​n.*99-13259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 152,170 control chromosomes in the GnomAD database, including 312 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 0.045 (312 hom., cov: 32)
• Consequence: PTH2R ENST00000419079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927960	NR_136588.1	n.506-13259C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000419079.1	n.*99-13259C>T		intron_variant	Intron 3 of 6	2		ENSP00000393930.1

Frequencies

GnomAD3 genomes AF: 0.0449 AC: 6829 AN: 152052 Hom.: 314 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.00518

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0374

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

GnomAD4 genome AF: 0.0449 AC: 6835 AN: 152170 Hom.: 312 Cov.: 32 AF XY: 0.0441 AC XY: 3283 AN XY: 74396

African (AFR) AF: 0.117 AC: 4872 AN: 41516

American (AMR) AF: 0.0221 AC: 337 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00950 AC: 33 AN: 3472

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5176

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4818

European-Finnish (FIN) AF: 0.00518 AC: 55 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 997 AN: 68002

Other (OTH) AF: 0.0365 AC: 77 AN: 2110

Alfa AF: 0.0208 Hom.: 92

Bravo AF: 0.0488

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10497908; hg19: chr2-209508291;