chr8-56958103-T-TG

Position:

• chr8-56958103-T-TG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_017813.5(BPNT2):​c.*5689dupC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 151,950 control chromosomes in the GnomAD database, including 30 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.015 (30 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BPNT2 NM_017813.5 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.341

Genes affected

BPNT2 (HGNC:26019): (3'(2'), 5'-bisphosphate nucleotidase 2) This gene encodes a member of the inositol monophosphatase family. The encoded protein is localized to the Golgi apparatus and catalyzes the hydrolysis of phosphoadenosine phosphate (PAP) to adenosine monophosphate (AMP). Mutations in this gene are a cause of GRAPP type chondrodysplasia with joint dislocations, and a pseudogene of this gene is located on the long arm of chromosome 1. [provided by RefSeq, Dec 2011]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-56958103-T-TG is Benign according to our data. Variant chr8-56958103-T-TG is described in ClinVar as [Likely_benign]. Clinvar id is 363324.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0148 (2249/151950) while in subpopulation SAS AF= 0.0321 (154/4802). AF 95% confidence interval is 0.0279. There are 30 homozygotes in gnomad4. There are 1050 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 30 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BPNT2	NM_017813.5	c.*5689dupC		3_prime_UTR_variant	5/5	ENST00000262644.9	NP_060283.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BPNT2	ENST00000262644	c.*5689dupC		3_prime_UTR_variant	5/5	1	NM_017813.5	ENSP00000262644.4

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2252 AN: 151834 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00395

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00965

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0318

Gnomad FIN AF: 0.00993

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0239

Gnomad OTH AF: 0.0187

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0148 AC: 2249 AN: 151950 Hom.: 30 Cov.: 32 AF XY: 0.0141 AC XY: 1050 AN XY: 74316

Gnomad4 AFR AF: 0.00393

Gnomad4 AMR AF: 0.00964

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.00993

Gnomad4 NFE AF: 0.0239

Gnomad4 OTH AF: 0.0176

Bravo AF: 0.0140

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Chondrodysplasia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs200630025; hg19: chr8-57870662;