ENST00000512223.6:c.339-77661G>C

Variant names:

• chr12-19642972-G-C
• rs11044734
• ENST00000512223.6:c.339-77661G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512223.6(AEBP2):​c.339-77661G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 150,356 control chromosomes in the GnomAD database, including 667 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 0.083 (667 hom., cov: 29)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 3 publications found

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]

LOC101928387 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928387	XR_001749035.2	n.526-7424G>C		intron_variant	Intron 1 of 3
LOC101928387	XR_001749036.2	n.526-6726G>C		intron_variant	Intron 1 of 4
LOC101928387	XR_007063236.1	n.472-7424G>C		intron_variant	Intron 3 of 6
LOC101928387	XR_007063237.1	n.928-7424G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-77661G>C		intron_variant	Intron 4 of 4	3		ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12515 AN: 150234 Hom.: 666 Cov.: 29

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.0630

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.0647

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0739

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

GnomAD4 genome AF: 0.0832 AC: 12516 AN: 150356 Hom.: 667 Cov.: 29 AF XY: 0.0835 AC XY: 6119 AN XY: 73322

African (AFR) AF: 0.0393 AC: 1604 AN: 40850

American (AMR) AF: 0.0628 AC: 947 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3458

East Asian (EAS) AF: 0.252 AC: 1270 AN: 5038

South Asian (SAS) AF: 0.0652 AC: 306 AN: 4696

European-Finnish (FIN) AF: 0.0988 AC: 1008 AN: 10200

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6598 AN: 67760

Other (OTH) AF: 0.0736 AC: 153 AN: 2080

Alfa AF: 0.0788 Hom.: 83

Bravo AF: 0.0797

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.81
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs11044734; hg19: chr12-19795906;