NM_001330701.2:c.3639A>C

Variant names:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001330701.2(AGTPBP1):c.3639A>C(p.Glu1213Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00555 in 1,613,038 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0041 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 44 hom. )

Consequence

AGTPBP1
NM_001330701.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.311

Variant links:

Genes affected

AGTPBP1 (HGNC:17258): (ATP/GTP binding carboxypeptidase 1) NNA1 is a zinc carboxypeptidase that contains nuclear localization signals and an ATP/GTP-binding motif that was initially cloned from regenerating spinal cord neurons of the mouse.[supplied by OMIM, Jul 2002]

AGTPBP1 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 (MetaRNN=0.0020323396).

BP6

Variant 9-85547151-T-G is Benign according to our data. Variant chr9-85547151-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2659286.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00414 (631/152328) while in subpopulation NFE AF= 0.0069 (469/68014). AF 95% confidence interval is 0.00638. There are 0 homozygotes in gnomad4. There are 282 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAdExome4 at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGTPBP1	NM_001330701.2 link	c.3639A>C	p.Glu1213Asp	missense_variant	Exon 26 of 26	ENST00000357081.8	NP_001317630.1	Q9UPW5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
AGTPBP1	ENST00000357081.8 link	c.3639A>C	p.Glu1213Asp	missense_variant	Exon 26 of 26	5	NM_001330701.2	ENSP00000349592.3	Q9UPW5-1
AGTPBP1	ENST00000376083.7 link	c.3519A>C	p.Glu1173Asp	missense_variant	Exon 26 of 26	1		ENSP00000365251.3	Q9UPW5-2
AGTPBP1	ENST00000337006.8 link	c.3795A>C	p.Glu1265Asp	missense_variant	Exon 25 of 25	5		ENSP00000338512.5	J3KNS1
AGTPBP1	ENST00000628899.1 link	c.3675A>C	p.Glu1225Asp	missense_variant	Exon 25 of 25	2		ENSP00000487074.1	Q9UPW5-3

Frequencies

GnomAD3 genomes

AF:

0.00415

AC:

631

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00419

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00689

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00474

AC:

1185

AN:

249974

Hom.:

AF XY:

0.00506

AC XY:

684

AN XY:

135214

show subpopulations

Gnomad AFR exome

AF:

0.000742

Gnomad AMR exome

AF:

0.00533

Gnomad ASJ exome

AF:

0.00657

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00207

Gnomad FIN exome

AF:

0.000741

Gnomad NFE exome

AF:

0.00717

Gnomad OTH exome

AF:

0.00575

GnomAD4 exome

AF:

0.00570

AC:

8323

AN:

1460710

Hom.:

Cov.:

AF XY:

0.00563

AC XY:

4091

AN XY:

726740

show subpopulations

Gnomad4 AFR exome

AF:

0.000958

Gnomad4 AMR exome

AF:

0.00531

Gnomad4 ASJ exome

AF:

0.00678

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00209

Gnomad4 FIN exome

AF:

0.000918

Gnomad4 NFE exome

AF:

0.00644

Gnomad4 OTH exome

AF:

0.00676

GnomAD4 genome

AF:

0.00414

AC:

631

AN:

152328

Hom.:

Cov.:

AF XY:

0.00379

AC XY:

282

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00418

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00208

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.00690

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00665

Hom.:

Bravo

AF:

0.00465

TwinsUK

AF:

0.00512

AC:

ALSPAC

AF:

0.00519

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00698

AC:

ExAC

AF:

0.00479

AC:

581

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00797

EpiControl

AF:

0.00856

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

AGTPBP1-related disorder

Benign:1

May 14, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Feb 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

AGTPBP1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.75

CADD

Benign

DANN

Benign

0.90

DEOGEN2

Benign

0.045

.;.;T;.

Eigen

Benign

-0.57

Eigen_PC

Benign

-0.34

FATHMM_MKL

Benign

0.66

LIST_S2

Benign

0.78

T;T;T;T

M_CAP

Benign

0.0036

MetaRNN

Benign

0.0020

T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

-0.74

.;.;N;.

PrimateAI

Benign

0.40

PROVEAN

Benign

0.040

N;.;N;.

REVEL

Benign

0.031

Sift

Benign

0.58

T;.;T;.

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0

B;.;B;B

Vest4

0.086

MutPred

0.095

.;.;Loss of solvent accessibility (P = 0.0152);.;

MVP

0.21

MPC

0.050

ClinPred

0.0017

GERP RS

2.3

Varity_R

0.051

gMVP

0.068

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