2-208382659-T-C

Position:

• chr2-208382659-T-C

Variant summary

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

The NM_001309516.2(PTH2R):​c.-259+22422T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,224 control chromosomes in the GnomAD database, including 63,137 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 0.90 (63137 hom., cov: 32)
• Consequence: PTH2R NM_001309516.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTH2R	NM_001309516.2	c.-259+22422T>C		intron_variant			NP_001296445.1
PTH2R	NM_001371905.1	c.-326+22422T>C		intron_variant			NP_001358834.1
PTH2R	NM_001371906.1	c.-335+22422T>C		intron_variant			NP_001358835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTH2R	ENST00000617735.4	c.-259+22422T>C		intron_variant		2		ENSP00000482485

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137300 AN: 152106 Hom.: 63099 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.903 AC: 137389 AN: 152224 Hom.: 63137 Cov.: 32 AF XY: 0.906 AC XY: 67404 AN XY: 74430

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.953

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.921

Alfa AF: 0.955 Hom.: 31882

Bravo AF: 0.892

Asia WGS AF: 0.932 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.74
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs920218; hg19: chr2-209247384;