chr7-44104602-C-G

Position:

• chr7-44104602-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001129.5(AEBP1):​c.-64C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,183,826 control chromosomes in the GnomAD database, including 38,215 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3754 hom., cov: 30)
  • Exomes 𝑓: 0.25 (34461 hom.)
• Consequence: AEBP1 NM_001129.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.17

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 7-44104602-C-G is Benign according to our data. Variant chr7-44104602-C-G is described in ClinVar as [Benign]. Clinvar id is 1248323.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AEBP1	NM_001129.5	c.-64C>G		5_prime_UTR_variant	1/21	ENST00000223357.8	NP_001120.3
AEBP1	XM_011515162.2	c.-64C>G		5_prime_UTR_variant	1/20		XP_011513464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP1	ENST00000223357.8	c.-64C>G		5_prime_UTR_variant	1/21	1	NM_001129.5	ENSP00000223357	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30420 AN: 151546 Hom.: 3755 Cov.: 30

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.238

GnomAD4 exome AF: 0.251 AC: 259358 AN: 1032172 Hom.: 34461 Cov.: 13 AF XY: 0.248 AC XY: 126147 AN XY: 508944

Gnomad4 AFR exome AF: 0.0407

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.262

Gnomad4 EAS exome AF: 0.198

Gnomad4 SAS exome AF: 0.0976

Gnomad4 FIN exome AF: 0.252

Gnomad4 NFE exome AF: 0.268

Gnomad4 OTH exome AF: 0.235

GnomAD4 genome AF: 0.201 AC: 30416 AN: 151654 Hom.: 3754 Cov.: 30 AF XY: 0.199 AC XY: 14763 AN XY: 74118

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.0971

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.238

Alfa AF: 0.218 Hom.: 500

Bravo AF: 0.202

Asia WGS AF: 0.148 AC: 514 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.84

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

Other links and lift over

dbSNP: rs28362520; hg19: chr7-44144201; COSMIC: COSV56258612; COSMIC: COSV56258612;