Variant 1-220062792-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_006085.6(BPNT1):c.637G>A(p.Asp213Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0031 in 1,614,148 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 3 hom., cov: 31)

Exomes 𝑓: 0.0030 ( 19 hom. )

Consequence

BPNT1
NM_006085.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.29

Variant links:

Genes affected

BPNT1 (HGNC:1096): (3'(2'), 5'-bisphosphate nucleotidase 1) BPNT1, also called bisphosphate 3-prime-nucleotidase, or BPntase, is a member of a magnesium-dependent phosphomonoesterase family. Lithium, a major drug used to treat manic depression, acts as an uncompetitive inhibitor of BPntase. The predicted human protein is 92% identical to mouse BPntase. BPntase's physiologic role in nucleotide metabolism may be regulated by inositol signaling pathways. The inhibition of human BPntase may account for lithium-induced nephrotoxicity. [provided by RefSeq, Jul 2008]

BPNT1 links:

BPNT1 (HGNC:):

BPNT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0064237416).

BP6

Variant 1-220062792-C-T is Benign according to our data. Variant chr1-220062792-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2639906.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPNT1	NM_006085.6 linkuse as main transcript	c.637G>A	p.Asp213Asn	missense_variant	7/9	ENST00000322067.12	NP_006076.4	O95861-1V9HWF9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BPNT1	ENST00000322067.12 linkuse as main transcript	c.637G>A	p.Asp213Asn	missense_variant	7/9	1	NM_006085.6	ENSP00000318852.7		O95861-1

Frequencies

GnomAD3 genomes

AF:

0.00376

AC:

572

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000386

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00236

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00979

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00592

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00332

AC:

829

AN:

249570

Hom.:

AF XY:

0.00342

AC XY:

463

AN XY:

135398

show subpopulations

Gnomad AFR exome

AF:

0.000323

Gnomad AMR exome

AF:

0.000782

Gnomad ASJ exome

AF:

0.000695

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.0101

Gnomad NFE exome

AF:

0.00480

Gnomad OTH exome

AF:

0.00429

GnomAD4 exome

AF:

0.00303

AC:

4435

AN:

1461874

Hom.:

Cov.:

AF XY:

0.00306

AC XY:

2226

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.000388

Gnomad4 AMR exome

AF:

0.000760

Gnomad4 ASJ exome

AF:

0.000383

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0000812

Gnomad4 FIN exome

AF:

0.0113

Gnomad4 NFE exome

AF:

0.00324

Gnomad4 OTH exome

AF:

0.00273

GnomAD4 genome

AF:

0.00376

AC:

572

AN:

152274

Hom.:

Cov.:

AF XY:

0.00364

AC XY:

271

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.000385

Gnomad4 AMR

AF:

0.00235

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00979

Gnomad4 NFE

AF:

0.00592

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00408

Hom.:

Bravo

AF:

0.00239

ESP6500AA

AF:

0.000254

AC:

ESP6500EA

AF:

0.00384

AC:

ExAC

AF:

0.00350

AC:

423

EpiCase

AF:

0.00403

EpiControl

AF:

0.00367

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2022

BPNT1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.32

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.15

.;.;T;T;T

Eigen

Uncertain

0.30

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.95

LIST_S2

Pathogenic

0.98

D;D;D;.;D

MetaRNN

Benign

0.0064

T;T;T;T;T

MetaSVM

Uncertain

0.13

MutationAssessor

Uncertain

2.1

.;.;M;M;.

PrimateAI

Uncertain

0.52

PROVEAN

Benign

-1.8

N;N;N;N;N

REVEL

Uncertain

0.39

Sift

Benign

0.067

T;T;T;T;T

Sift4G

Benign

0.15

T;T;T;T;T

Polyphen

0.63, 0.98

.;.;P;P;D

Vest4

0.32

MVP

0.62

MPC

0.62

ClinPred

0.039

GERP RS

5.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.38

gMVP

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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