chr12-19491592-G-A

Variant names:

• chr12-19491592-G-A
• rs7305762
• NM_153207.5:c.988-2208G>A

Variant summary

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

The NM_153207.5(AEBP2):​c.988-2208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,088 control chromosomes in the GnomAD database, including 54,056 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 (54056 hom., cov: 31)
• Consequence: AEBP2 NM_153207.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AEBP2	NM_153207.5	c.988-2208G>A		intron_variant	Intron 3 of 7	ENST00000266508.14	NP_694939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000266508.14	c.988-2208G>A		intron_variant	Intron 3 of 7	1	NM_153207.5	ENSP00000266508.9

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127881 AN: 151970 Hom.: 54007 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.842 AC: 127987 AN: 152088 Hom.: 54056 Cov.: 31 AF XY: 0.842 AC XY: 62625 AN XY: 74344

African (AFR) AF: 0.900 AC: 37346 AN: 41496

American (AMR) AF: 0.789 AC: 12044 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2661 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4348 AN: 5174

South Asian (SAS) AF: 0.750 AC: 3602 AN: 4804

European-Finnish (FIN) AF: 0.865 AC: 9144 AN: 10574

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.825 AC: 56091 AN: 67996

Other (OTH) AF: 0.820 AC: 1732 AN: 2112

Alfa AF: 0.820 Hom.: 84613

Bravo AF: 0.837

Asia WGS AF: 0.809 AC: 2808 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		0.099
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: rs7305762; hg19: chr12-19644526;