chr2-208477369-A-G

Position:

• chr2-208477369-A-G

Variant summary

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

The NM_005048.4(PTH2R):​c.982-3701A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,154 control chromosomes in the GnomAD database, including 48,792 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 0.80 (48792 hom., cov: 32)
• Consequence: PTH2R NM_005048.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTH2R	NM_005048.4	c.982-3701A>G		intron_variant		ENST00000272847.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTH2R	ENST00000272847.7	c.982-3701A>G		intron_variant		1	NM_005048.4	P1
	ENST00000424628.1	n.103+7417A>G		intron_variant, non_coding_transcript_variant		4
PTH2R	ENST00000617735.4	c.649-3701A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121265 AN: 152036 Hom.: 48751 Cov.: 32

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.798 AC: 121366 AN: 152154 Hom.: 48792 Cov.: 32 AF XY: 0.797 AC XY: 59267 AN XY: 74372

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.783

Alfa AF: 0.783 Hom.: 62080

Bravo AF: 0.799

Asia WGS AF: 0.679 AC: 2361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs897083; hg19: chr2-209342094;