rs34406824

Positions:

• chr1-220060054-T-C

Variant summary

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

The NM_006085.6(BPNT1):​c.673-263A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,256 control chromosomes in the GnomAD database, including 229 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 0.050 (229 hom., cov: 32)
• Consequence: BPNT1 NM_006085.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPNT1	NM_006085.6	c.673-263A>G		intron_variant		ENST00000322067.12	NP_006076.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BPNT1	ENST00000322067.12	c.673-263A>G		intron_variant		1	NM_006085.6	ENSP00000318852.7

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7546 AN: 152138 Hom.: 220 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0415

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0425

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0525

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

GnomAD4 genome AF: 0.0498 AC: 7579 AN: 152256 Hom.: 229 Cov.: 32 AF XY: 0.0486 AC XY: 3616 AN XY: 74450

Gnomad4 AFR AF: 0.0702

Gnomad4 AMR AF: 0.0414

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0421

Gnomad4 FIN AF: 0.0115

Gnomad4 NFE AF: 0.0397

Gnomad4 OTH AF: 0.0548

Alfa AF: 0.0425 Hom.: 38

Bravo AF: 0.0540

Asia WGS AF: 0.0760 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.53

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: rs34406824; hg19: chr1-220233396;