12-19715998-G-T

Position:

• chr12-19715998-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512223.6(AEBP2):​c.339-4635G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,098 control chromosomes in the GnomAD database, including 3,304 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 0.18 (3304 hom., cov: 32)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.547

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-4635G>T		intron_variant		3		ENSP00000445587

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27701 AN: 151980 Hom.: 3304 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.182 AC: 27697 AN: 152098 Hom.: 3304 Cov.: 32 AF XY: 0.181 AC XY: 13493 AN XY: 74372

Gnomad4 AFR AF: 0.0523

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.00367

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.194

Alfa AF: 0.223 Hom.: 1942

Bravo AF: 0.169

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7300261; hg19: chr12-19868932;