2-208713876-T-G

Variant names:

• chr2-208713876-T-G
• rs13383928
• ENST00000419079.1:n.*262+56887T>G

Variant summary

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

The ENST00000419079.1(PTH2R):​n.*262+56887T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,032 control chromosomes in the GnomAD database, including 753 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 0.077 (753 hom., cov: 32)
• Consequence: PTH2R ENST00000419079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 10 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927960	NR_136588.1	n.669+56887T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000419079.1	n.*262+56887T>G		intron_variant	Intron 4 of 6	2		ENSP00000393930.1

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11651 AN: 151914 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00890

Gnomad FIN AF: 0.0573

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0767 AC: 11661 AN: 152032 Hom.: 753 Cov.: 32 AF XY: 0.0744 AC XY: 5532 AN XY: 74316

African (AFR) AF: 0.172 AC: 7124 AN: 41492

American (AMR) AF: 0.0377 AC: 574 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4826

European-Finnish (FIN) AF: 0.0573 AC: 607 AN: 10600

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0429 AC: 2916 AN: 67922

Other (OTH) AF: 0.0699 AC: 148 AN: 2116

Alfa AF: 0.0515 Hom.: 448

Bravo AF: 0.0793

Asia WGS AF: 0.0130 AC: 44 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs13383928; hg19: chr2-209578600;