rs10505838

Positions:

• chr12-19530786-A-C

Variant summary

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

The ENST00000398731.3(AEBP2):​c.302+12673A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,256 control chromosomes in the GnomAD database, including 458 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 0.070 (458 hom., cov: 32)
• Consequence: AEBP2 ENST00000398731.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.19530786A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000398731.3	c.302+12673A>C		intron_variant		3		ENSP00000381715.2
AEBP2	ENST00000512223.6	c.338+12673A>C		intron_variant		3		ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10721 AN: 152138 Hom.: 455 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0671

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0705 AC: 10727 AN: 152256 Hom.: 458 Cov.: 32 AF XY: 0.0721 AC XY: 5369 AN XY: 74444

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.0671

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0755

Gnomad4 OTH AF: 0.0686

Alfa AF: 0.0810 Hom.: 316

Bravo AF: 0.0651

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505838; hg19: chr12-19683720;