12-19648661-G-T

Variant names:

• chr12-19648661-G-T
• rs6486986
• ENST00000512223.6:c.339-71972G>T

Variant summary

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

The ENST00000512223.6(AEBP2):​c.339-71972G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,170 control chromosomes in the GnomAD database, including 54,240 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 0.84 (54240 hom., cov: 32)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512223.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AEBP2	ENST00000512223.6	TSL:3	c.339-71972G>T		intron	N/A	ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127741 AN: 152052 Hom.: 54191 Cov.: 32

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.840 AC: 127844 AN: 152170 Hom.: 54240 Cov.: 32 AF XY: 0.831 AC XY: 61802 AN XY: 74394

African (AFR) AF: 0.919 AC: 38170 AN: 41532

American (AMR) AF: 0.799 AC: 12214 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3042 AN: 3470

East Asian (EAS) AF: 0.578 AC: 2975 AN: 5146

South Asian (SAS) AF: 0.595 AC: 2872 AN: 4826

European-Finnish (FIN) AF: 0.801 AC: 8483 AN: 10584

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57257 AN: 68004

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

Alfa AF: 0.839 Hom.: 161251

Bravo AF: 0.843

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.28
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs6486986; hg19: chr12-19801595;