chr12-19444421-A-G

Variant names:

• chr12-19444421-A-G
• rs12824219
• NM_153207.5:c.671+4051A>G

Variant summary

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

The NM_153207.5(AEBP2):​c.671+4051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,294 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 33)
• Consequence: AEBP2 NM_153207.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 1 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=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AEBP2	NM_153207.5	c.671+4051A>G		intron_variant	Intron 1 of 7	ENST00000266508.14	NP_694939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000266508.14	c.671+4051A>G		intron_variant	Intron 1 of 7	1	NM_153207.5	ENSP00000266508.9

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15844 AN: 152176 Hom.: 845 Cov.: 33

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.0968

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0192

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.104 AC: 15843 AN: 152294 Hom.: 842 Cov.: 33 AF XY: 0.103 AC XY: 7674 AN XY: 74468

African (AFR) AF: 0.0811 AC: 3372 AN: 41562

American (AMR) AF: 0.0966 AC: 1478 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5188

South Asian (SAS) AF: 0.120 AC: 577 AN: 4828

European-Finnish (FIN) AF: 0.0940 AC: 997 AN: 10612

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8418 AN: 68016

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.105 Hom.: 157

Bravo AF: 0.101

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.0
DANN	Benign	0.89
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12824219; hg19: chr12-19597355;