12-19544697-T-C

Variant names:

• chr12-19544697-T-C
• rs2900433
• ENST00000398731.3:c.303-8156T>C

Variant summary

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

The ENST00000398731.3(AEBP2):​c.303-8156T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,130 control chromosomes in the GnomAD database, including 53,185 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 0.83 (53185 hom., cov: 32)
• Consequence: AEBP2 ENST00000398731.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000398731.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AEBP2	ENST00000398731.3	TSL:3	c.303-8156T>C		intron	N/A	ENSP00000381715.2	H7BYT4
	AEBP2	ENST00000512223.6	TSL:3	c.338+26584T>C		intron	N/A	ENSP00000445587.1	H0YH08

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126924 AN: 152012 Hom.: 53142 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.835 AC: 127025 AN: 152130 Hom.: 53185 Cov.: 32 AF XY: 0.836 AC XY: 62193 AN XY: 74384

African (AFR) AF: 0.877 AC: 36408 AN: 41492

American (AMR) AF: 0.787 AC: 12023 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2662 AN: 3472

East Asian (EAS) AF: 0.841 AC: 4329 AN: 5150

South Asian (SAS) AF: 0.748 AC: 3604 AN: 4820

European-Finnish (FIN) AF: 0.864 AC: 9154 AN: 10594

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56113 AN: 68008

Other (OTH) AF: 0.815 AC: 1717 AN: 2108

Alfa AF: 0.822 Hom.: 77891

Bravo AF: 0.830

Asia WGS AF: 0.802 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2900433; hg19: chr12-19697631;