chr2-208625881-A-G

Variant names:

• chr2-208625881-A-G
• rs10497906
• ENST00000419079.1:n.*99-30945A>G

Variant summary

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

The ENST00000419079.1(PTH2R):​n.*99-30945A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 151,680 control chromosomes in the GnomAD database, including 781 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 0.065 (781 hom., cov: 32)
• Consequence: PTH2R ENST00000419079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927960	NR_136588.1	n.506-30945A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000419079.1	n.*99-30945A>G		intron_variant	Intron 3 of 6	2		ENSP00000393930.1

Frequencies

GnomAD3 genomes AF: 0.0654 AC: 9914 AN: 151562 Hom.: 785 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.00953

Gnomad EAS AF: 0.0276

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0476

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

GnomAD4 genome AF: 0.0654 AC: 9922 AN: 151680 Hom.: 781 Cov.: 32 AF XY: 0.0644 AC XY: 4773 AN XY: 74160

African (AFR) AF: 0.189 AC: 7840 AN: 41456

American (AMR) AF: 0.0284 AC: 431 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.00953 AC: 33 AN: 3462

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5172

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4830

European-Finnish (FIN) AF: 0.00452 AC: 48 AN: 10616

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

European-Non Finnish (NFE) AF: 0.0147 AC: 996 AN: 67646

Other (OTH) AF: 0.0466 AC: 98 AN: 2104

Alfa AF: 0.0433 Hom.: 65

Bravo AF: 0.0721

Asia WGS AF: 0.0560 AC: 196 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	10
DANN	Benign	0.92
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10497906; hg19: chr2-209490605;