chr12-19626859-T-C

Variant names:

• chr12-19626859-T-C
• rs10841287
• ENST00000512223.6:c.339-93774T>C

Variant summary

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

The ENST00000512223.6(AEBP2):​c.339-93774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,016 control chromosomes in the GnomAD database, including 9,679 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 0.31 (9679 hom., cov: 32)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AEBP2	ENST00000512223.6	TSL:3	c.339-93774T>C		intron	N/A	ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47731 AN: 151898 Hom.: 9653 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.314 AC: 47797 AN: 152016 Hom.: 9679 Cov.: 32 AF XY: 0.310 AC XY: 23033 AN XY: 74302

African (AFR) AF: 0.585 AC: 24227 AN: 41410

American (AMR) AF: 0.188 AC: 2879 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1550 AN: 5160

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2401 AN: 10582

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14159 AN: 67990

Other (OTH) AF: 0.261 AC: 549 AN: 2104

Alfa AF: 0.233 Hom.: 19407

Bravo AF: 0.322

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.56
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10841287; hg19: chr12-19779793;