Variant chr11-13492716-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000315.4(PTH):c.87-50G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,613,372 control chromosomes in the GnomAD database, including 85,603 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 6236 hom., cov: 32)

Exomes 𝑓: 0.32 ( 79367 hom. )

Consequence

PTH
NM_000315.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.298

Variant links:

Genes affected

PTH (HGNC:9606): (parathyroid hormone) This gene encodes a member of the parathyroid family of proteins. The encoded preproprotein is proteolytically processed to generate a protein that binds to the parathyroid hormone/parathyroid hormone-related peptide receptor and regulates blood calcium and phosphate levels. Excess production of the encoded protein, known as hyperparathyroidism, can result in hypercalcemia and kidney stones. On the other hand, defective processing of the encoded protein may lead to hypoparathyroidism, which can result in hypocalcemia and numbness. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]

PTH links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 11-13492716-C-T is Benign according to our data. Variant chr11-13492716-C-T is described in ClinVar as [Benign]. Clinvar id is 1289830.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTH	NM_000315.4 linkuse as main transcript	c.87-50G>A		intron_variant		ENST00000282091.6
PTH	NM_001316352.2 linkuse as main transcript	c.183-50G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTH	ENST00000282091.6 linkuse as main transcript	c.87-50G>A		intron_variant		1	NM_000315.4	P1
PTH	ENST00000529816.1 linkuse as main transcript	c.87-50G>A		intron_variant		5		P1

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39613

AN:

151932

Hom.:

6240

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0929

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.259

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.351

Gnomad OTH

AF:

0.260

GnomAD3 exomes

AF:

0.283

AC:

70884

AN:

250436

Hom.:

11350

AF XY:

0.286

AC XY:

38709

AN XY:

135336

show subpopulations

Gnomad AFR exome

AF:

0.0871

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.304

Gnomad EAS exome

AF:

0.116

Gnomad SAS exome

AF:

0.192

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.354

Gnomad OTH exome

AF:

0.314

GnomAD4 exome

AF:

0.321

AC:

469593

AN:

1461322

Hom.:

79367

Cov.:

AF XY:

0.319

AC XY:

231828

AN XY:

726924

show subpopulations

Gnomad4 AFR exome

AF:

0.0820

Gnomad4 AMR exome

AF:

0.224

Gnomad4 ASJ exome

AF:

0.302

Gnomad4 EAS exome

AF:

0.104

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.402

Gnomad4 NFE exome

AF:

0.348

Gnomad4 OTH exome

AF:

0.294

GnomAD4 genome

AF:

0.261

AC:

39612

AN:

152050

Hom.:

6236

Cov.:

AF XY:

0.261

AC XY:

19398

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.0929

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.299

Gnomad4 EAS

AF:

0.117

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.421

Gnomad4 NFE

AF:

0.351

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.311

Hom.:

8826

Bravo

AF:

0.241

Asia WGS

AF:

0.156

AC:

543

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.6

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over