Variant 11-3811027-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_014489.4(PGAP2):c.-10-223G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,120 control chromosomes in the GnomAD database, including 30,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.60 ( 30523 hom., cov: 32)

Consequence

PGAP2
NM_014489.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.382

Variant links:

Genes affected

PGAP2 (HGNC:17893): (post-GPI attachment to proteins 2) The protein encoded by this gene plays a role in the maturation of glycosylphosphatidylinositol (GPI) anchors on GPI-anchored proteins. Mutations in this gene are associated with an autosomal recessive syndrome characterized by hyperphosphatasia and intellectual disability. [provided by RefSeq, Jul 2017]

PGAP2 links:

PGAP2 (HGNC:):

PGAP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 11-3811027-G-T is Benign according to our data. Variant chr11-3811027-G-T is described in ClinVar as [Benign]. Clinvar id is 1236447.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGAP2	NM_014489.4 linkuse as main transcript	c.-10-223G>T		intron_variant		ENST00000278243.9	NP_055304.1	Q9UHJ9-2A0A024RCC6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGAP2	ENST00000278243.9 linkuse as main transcript	c.-10-223G>T		intron_variant		1	NM_014489.4	ENSP00000278243.4		Q9UHJ9-2

Frequencies

GnomAD3 genomes

AF:

0.602

AC:

91470

AN:

152004

Hom.:

30528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.298

Gnomad AMI

AF:

0.645

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.784

Gnomad SAS

AF:

0.682

Gnomad FIN

AF:

0.787

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.633

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

GnomAD4 genome

AF:

0.601

AC:

91484

AN:

152120

Hom.:

30523

Cov.:

AF XY:

0.603

AC XY:

44826

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.297

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.784

Gnomad4 SAS

AF:

0.682

Gnomad4 FIN

AF:

0.787

Gnomad4 NFE

AF:

0.739

Gnomad4 OTH

AF:

0.634

Alfa

AF:

0.644

Hom.:

6396

Bravo

AF:

0.569

Asia WGS

AF:

0.697

AC:

2424

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.77

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