Variant 7-44104685-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001129.5(AEBP1):c.20C>A(p.Ala7Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 1,551,786 control chromosomes in the GnomAD database, including 636 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.018 ( 35 hom., cov: 32)

Exomes 𝑓: 0.027 ( 601 hom. )

Consequence

AEBP1
NM_001129.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.258

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=0.0021805167).

BP6

Variant 7-44104685-C-A is Benign according to our data. Variant chr7-44104685-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1197858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AEBP1	NM_001129.5 linkuse as main transcript	c.20C>A	p.Ala7Glu	missense_variant	1/21	ENST00000223357.8
AEBP1	XM_011515162.2 linkuse as main transcript	c.20C>A	p.Ala7Glu	missense_variant	1/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AEBP1	ENST00000223357.8 linkuse as main transcript	c.20C>A	p.Ala7Glu	missense_variant	1/21	1	NM_001129.5	P1	Q8IUX7-1

Frequencies

GnomAD3 genomes

AF:

0.0185

AC:

2806

AN:

152050

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00509

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0119

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.0286

Gnomad FIN

AF:

0.0289

Gnomad MID

AF:

0.0223

Gnomad NFE

AF:

0.0263

Gnomad OTH

AF:

0.0167

GnomAD3 exomes

AF:

0.0233

AC:

3972

AN:

170248

Hom.:

AF XY:

0.0242

AC XY:

2315

AN XY:

95514

show subpopulations

Gnomad AFR exome

AF:

0.00444

Gnomad AMR exome

AF:

0.00978

Gnomad ASJ exome

AF:

0.0120

Gnomad EAS exome

AF:

0.0223

Gnomad SAS exome

AF:

0.0310

Gnomad FIN exome

AF:

0.0306

Gnomad NFE exome

AF:

0.0277

Gnomad OTH exome

AF:

0.0207

GnomAD4 exome

AF:

0.0270

AC:

37780

AN:

1399624

Hom.:

601

Cov.:

AF XY:

0.0270

AC XY:

18680

AN XY:

692816

show subpopulations

Gnomad4 AFR exome

AF:

0.00337

Gnomad4 AMR exome

AF:

0.0106

Gnomad4 ASJ exome

AF:

0.0116

Gnomad4 EAS exome

AF:

0.0650

Gnomad4 SAS exome

AF:

0.0286

Gnomad4 FIN exome

AF:

0.0280

Gnomad4 NFE exome

AF:

0.0274

Gnomad4 OTH exome

AF:

0.0227

GnomAD4 genome

AF:

0.0184

AC:

2803

AN:

152162

Hom.:

Cov.:

AF XY:

0.0185

AC XY:

1374

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.00508

Gnomad4 AMR

AF:

0.0119

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.0211

Gnomad4 SAS

AF:

0.0280

Gnomad4 FIN

AF:

0.0289

Gnomad4 NFE

AF:

0.0263

Gnomad4 OTH

AF:

0.0166

Alfa

AF:

0.0131

Hom.:

Bravo

AF:

0.0163

TwinsUK

AF:

0.0256

AC:

ALSPAC

AF:

0.0291

AC:

112

ESP6500AA

AF:

0.00424

AC:

ESP6500EA

AF:

0.0217

AC:

182

ExAC

AF:

0.0180

AC:

2079

Asia WGS

AF:

0.0180

AC:

AN:

3474

ClinVar

Significance: Benign/Likely 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	clinical testing	Invitae	Jan 31, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 22, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.22

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.082

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.35

FATHMM_MKL

Benign

0.16

LIST_S2

Benign

0.48

MetaRNN

Benign

0.0022

MetaSVM

Uncertain

-0.14

MutationAssessor

Benign

0.55

MutationTaster

Benign

0.75

PrimateAI

Uncertain

0.75

PROVEAN

Benign

-0.30

REVEL

Uncertain

0.29

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.50

Vest4

0.21

MPC

0.98

ClinPred

0.033

GERP RS

3.4

Varity_R

0.34

gMVP

0.68

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