Variant 10-16484555-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000535784.7(PTER):c.171A>G(p.Leu57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00391 in 1,614,086 control chromosomes in the GnomAD database, including 141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.016 ( 69 hom., cov: 32)

Exomes 𝑓: 0.0026 ( 72 hom. )

Consequence

PTER
ENST00000535784.7 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.06

Variant links:

Genes affected

PTER (HGNC:9590): (phosphotriesterase related) Predicted to enable hydrolase activity, acting on ester bonds and zinc ion binding activity. Involved in epithelial cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

PTER links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 10-16484555-A-G is Benign according to our data. Variant chr10-16484555-A-G is described in ClinVar as [Benign]. Clinvar id is 785308.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.07 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0516 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTER	NM_001261836.2 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	2/5	ENST00000535784.7	NP_001248765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTER	ENST00000535784.7 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	2/5	1	NM_001261836.2	ENSP00000439485	P1	Q96BW5-1
PTER	ENST00000378000.5 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	3/6	1		ENSP00000367239	P1	Q96BW5-1
PTER	ENST00000298942.4 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	1/3	5		ENSP00000298942		Q96BW5-2
PTER	ENST00000423462.6 linkuse as main transcript	c.-15-1797A>G		intron_variant		3		ENSP00000389535

Frequencies

GnomAD3 genomes

AF:

0.0162

AC:

2468

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0534

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00656

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00518

Gnomad FIN

AF:

0.000660

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00104

Gnomad OTH

AF:

0.0148

GnomAD3 exomes

AF:

0.00560

AC:

1406

AN:

251270

Hom.:

AF XY:

0.00454

AC XY:

617

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.0561

Gnomad AMR exome

AF:

0.00275

Gnomad ASJ exome

AF:

0.00655

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00510

Gnomad FIN exome

AF:

0.000970

Gnomad NFE exome

AF:

0.00116

Gnomad OTH exome

AF:

0.00392

GnomAD4 exome

AF:

0.00262

AC:

3836

AN:

1461866

Hom.:

Cov.:

AF XY:

0.00260

AC XY:

1894

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0590

Gnomad4 AMR exome

AF:

0.00309

Gnomad4 ASJ exome

AF:

0.00551

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00490

Gnomad4 FIN exome

AF:

0.000618

Gnomad4 NFE exome

AF:

0.000657

Gnomad4 OTH exome

AF:

0.00517

GnomAD4 genome

AF:

0.0163

AC:

2476

AN:

152220

Hom.:

Cov.:

AF XY:

0.0161

AC XY:

1200

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0535

Gnomad4 AMR

AF:

0.00648

Gnomad4 ASJ

AF:

0.00605

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00497

Gnomad4 FIN

AF:

0.000660

Gnomad4 NFE

AF:

0.00104

Gnomad4 OTH

AF:

0.0147

Alfa

AF:

0.00441

Hom.:

Bravo

AF:

0.0181

Asia WGS

AF:

0.00693

AC:

AN:

3478

EpiCase

AF:

0.00202

EpiControl

AF:

0.00225

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	Mar 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

7.2

DANN

Benign

0.51

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

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