ENST00000512223.6:c.339-71814G>A

Variant names:

• chr12-19648819-G-A
• rs11044737
• ENST00000512223.6:c.339-71814G>A

Variant summary

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

The ENST00000512223.6(AEBP2):​c.339-71814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0969 in 152,098 control chromosomes in the GnomAD database, including 809 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 0.097 (809 hom., cov: 31)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 6 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 = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928387	XR_001749035.2	n.526-1577G>A		intron_variant	Intron 1 of 3
LOC101928387	XR_001749036.2	n.526-879G>A		intron_variant	Intron 1 of 4
LOC101928387	XR_007063236.1	n.472-1577G>A		intron_variant	Intron 3 of 6
LOC101928387	XR_007063237.1	n.928-1577G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-71814G>A		intron_variant	Intron 4 of 4	3		ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14727 AN: 151980 Hom.: 807 Cov.: 31

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0969 AC: 14733 AN: 152098 Hom.: 809 Cov.: 31 AF XY: 0.0972 AC XY: 7225 AN XY: 74332

African (AFR) AF: 0.0862 AC: 3576 AN: 41504

American (AMR) AF: 0.0711 AC: 1087 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1284 AN: 5158

South Asian (SAS) AF: 0.0665 AC: 320 AN: 4814

European-Finnish (FIN) AF: 0.100 AC: 1058 AN: 10564

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0969 AC: 6587 AN: 67992

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.0971 Hom.: 3435

Bravo AF: 0.0952

Asia WGS AF: 0.134 AC: 465 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	1.8
DANN	Benign	0.64
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11044737; hg19: chr12-19801753;