rs13898

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001129.5(AEBP1):c.3442G>A(p.Val1148Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0305 in 1,611,706 control chromosomes in the GnomAD database, including 912 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.021 ( 57 hom., cov: 33)

Exomes 𝑓: 0.031 ( 855 hom. )

Consequence

AEBP1
NM_001129.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.83

Variant links:

Genes affected

AEBP1 (HGNC:303): (AE binding protein 1) This gene encodes a member of carboxypeptidase A protein family. The encoded protein may function as a transcriptional repressor and play a role in adipogenesis and smooth muscle cell differentiation. Studies in mice suggest that this gene functions in wound healing and abdominal wall development. Overexpression of this gene is associated with glioblastoma. [provided by RefSeq, May 2013]

AEBP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0053476095).

BP6

Variant 7-44114226-G-A is Benign according to our data. Variant chr7-44114226-G-A is described in ClinVar as [Benign]. Clinvar id is 1226463.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0212 (3184/150028) while in subpopulation NFE AF= 0.0355 (2387/67236). AF 95% confidence interval is 0.0343. There are 57 homozygotes in gnomad4. There are 1497 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 57 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AEBP1	NM_001129.5 link	c.3442G>A	p.Val1148Ile	missense_variant	Exon 21 of 21	ENST00000223357.8	NP_001120.3	Q8IUX7-1
AEBP1	XM_011515162.2 link	c.3364G>A	p.Val1122Ile	missense_variant	Exon 20 of 20		XP_011513464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
AEBP1	ENST00000223357.8 link	c.3442G>A	p.Val1148Ile	missense_variant	Exon 21 of 21	1	NM_001129.5	ENSP00000223357.3	Q8IUX7-1
AEBP1	ENST00000450684.2 link	c.2167G>A	p.Val723Ile	missense_variant	Exon 8 of 8	2		ENSP00000398878.2	Q8IUX7-2
AEBP1	ENST00000413907.1 link	n.*1639G>A		non_coding_transcript_exon_variant	Exon 8 of 8	2		ENSP00000410349.1	H7C391
AEBP1	ENST00000413907.1 link	n.*1639G>A		3_prime_UTR_variant	Exon 8 of 8	2		ENSP00000410349.1	H7C391

Frequencies

GnomAD3 genomes

AF:

0.0212

AC:

3182

AN:

149910

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00614

Gnomad AMI

AF:

0.00773

Gnomad AMR

AF:

0.0154

Gnomad ASJ

AF:

0.0148

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00762

Gnomad FIN

AF:

0.0161

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.0355

Gnomad OTH

AF:

0.0228

GnomAD3 exomes

AF:

0.0205

AC:

5142

AN:

251340

Hom.:

AF XY:

0.0210

AC XY:

2851

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.00609

Gnomad AMR exome

AF:

0.0118

Gnomad ASJ exome

AF:

0.0155

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00924

Gnomad FIN exome

AF:

0.0156

Gnomad NFE exome

AF:

0.0328

Gnomad OTH exome

AF:

0.0222

GnomAD4 exome

AF:

0.0315

AC:

46034

AN:

1461678

Hom.:

855

Cov.:

AF XY:

0.0309

AC XY:

22498

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.00463

Gnomad4 AMR exome

AF:

0.0126

Gnomad4 ASJ exome

AF:

0.0161

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00951

Gnomad4 FIN exome

AF:

0.0165

Gnomad4 NFE exome

AF:

0.0374

Gnomad4 OTH exome

AF:

0.0253

GnomAD4 genome

AF:

0.0212

AC:

3184

AN:

150028

Hom.:

Cov.:

AF XY:

0.0204

AC XY:

1497

AN XY:

73320

show subpopulations

Gnomad4 AFR

AF:

0.00612

Gnomad4 AMR

AF:

0.0154

Gnomad4 ASJ

AF:

0.0148

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00805

Gnomad4 FIN

AF:

0.0161

Gnomad4 NFE

AF:

0.0355

Gnomad4 OTH

AF:

0.0226

Alfa

AF:

0.0294

Hom.:

165

Bravo

AF:

0.0203

TwinsUK

AF:

0.0431

AC:

160

ALSPAC

AF:

0.0436

AC:

168

ESP6500AA

AF:

0.00953

AC:

ESP6500EA

AF:

0.0372

AC:

320

ExAC

AF:

0.0210

AC:

2546

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.0293

EpiControl

AF:

0.0318

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 11, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.081

T;.

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.27

FATHMM_MKL

Uncertain

0.80

LIST_S2

Benign

0.52

T;T

MetaRNN

Benign

0.0053

T;T

MetaSVM

Uncertain

-0.22

MutationAssessor

Benign

0.97

L;.

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.16

N;N

REVEL

Benign

0.22

Sift

Uncertain

0.014

D;D

Sift4G

Benign

0.096

T;T

Polyphen

0.0020

B;B

Vest4

0.25

MPC

0.30

ClinPred

0.0067

GERP RS

4.2

Varity_R

0.11

gMVP

0.48

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