Variant 1-96769734-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_021190.4(PTBP2):c.147A>G(p.Gly49Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00216 in 1,603,394 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0022 ( 15 hom. )

Consequence

PTBP2
NM_021190.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.24

Variant links:

Genes affected

PTBP2 (HGNC:17662): (polypyrimidine tract binding protein 2) The protein encoded by this gene binds to intronic polypyrimidine clusters in pre-mRNA molecules and is implicated in controlling the assembly of other splicing-regulatory proteins. This protein is very similar to the polypyrimidine tract binding protein (PTB) but most of its isoforms are expressed primarily in the brain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

PTBP2 links:

PTBP2 (HGNC:):

PTBP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 1-96769734-A-G is Benign according to our data. Variant chr1-96769734-A-G is described in ClinVar as [Benign]. Clinvar id is 713770.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.24 with no splicing effect.

BS2

High AC in GnomAd4 at 309 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTBP2	NM_021190.4 linkuse as main transcript	c.147A>G	p.Gly49Gly	synonymous_variant	4/14	ENST00000674951.1	NP_067013.1	Q9UKA9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTBP2	ENST00000674951.1 linkuse as main transcript	c.147A>G	p.Gly49Gly	synonymous_variant	4/14		NM_021190.4	ENSP00000502818.1		Q9UKA9-1

Frequencies

GnomAD3 genomes

AF:

0.00203

AC:

308

AN:

152008

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.00177

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00993

Gnomad FIN

AF:

0.0000944

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00230

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00259

AC:

629

AN:

243088

Hom.:

AF XY:

0.00300

AC XY:

395

AN XY:

131592

show subpopulations

Gnomad AFR exome

AF:

0.000443

Gnomad AMR exome

AF:

0.00151

Gnomad ASJ exome

AF:

0.00727

Gnomad EAS exome

AF:

0.0000562

Gnomad SAS exome

AF:

0.00635

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00261

Gnomad OTH exome

AF:

0.00395

GnomAD4 exome

AF:

0.00217

AC:

3151

AN:

1451270

Hom.:

Cov.:

AF XY:

0.00238

AC XY:

1715

AN XY:

721832

show subpopulations

Gnomad4 AFR exome

AF:

0.000182

Gnomad4 AMR exome

AF:

0.00153

Gnomad4 ASJ exome

AF:

0.00638

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.00648

Gnomad4 FIN exome

AF:

0.000282

Gnomad4 NFE exome

AF:

0.00190

Gnomad4 OTH exome

AF:

0.00304

GnomAD4 genome

AF:

0.00203

AC:

309

AN:

152124

Hom.:

Cov.:

AF XY:

0.00202

AC XY:

150

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.000337

Gnomad4 AMR

AF:

0.00177

Gnomad4 ASJ

AF:

0.00720

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0101

Gnomad4 FIN

AF:

0.0000944

Gnomad4 NFE

AF:

0.00230

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00263

Hom.:

Bravo

AF:

0.00183

Asia WGS

AF:

0.000867

AC:

AN:

3476

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	Labcorp Genetics (formerly Invitae), Labcorp	Jun 20, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.73

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