rs4762767

chr12-19713195-A-Gchr12-19713195-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512223.6(AEBP2):c.339-7438A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,048 control chromosomes in the GnomAD database, including 37,248 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (37248 hom., cov: 32)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

Genes affected

AEBP2 (HGNC:24051): (AE binding protein 2) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Located in nucleoplasm. Part of ESC/E(Z) complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-7438A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105884 AN: 151932 Hom.: 37230 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.697 AC: 105942 AN: 152048 Hom.: 37248 Cov.: 32 AF XY: 0.698 AC XY: 51918 AN XY: 74338

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.706

Alfa AF: 0.725 Hom.: 45482

Bravo AF: 0.692

Asia WGS AF: 0.745 AC: 2591 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4762767; hg19: chr12-19866129;