rs10505839

Positions:

• chr12-19508046-A-C
• chr12-19508046-A-T

Variant summary

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

The NM_153207.5(AEBP2):​c.1300-4352A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0482 in 152,170 control chromosomes in the GnomAD database, including 389 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 0.048 (389 hom., cov: 32)
• Consequence: AEBP2 NM_153207.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AEBP2	NM_153207.5	c.1300-4352A>C		intron_variant		ENST00000266508.14	NP_694939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000266508.14	c.1300-4352A>C		intron_variant		1	NM_153207.5	ENSP00000266508.9

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7326 AN: 152052 Hom.: 388 Cov.: 32

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0482 AC: 7341 AN: 152170 Hom.: 389 Cov.: 32 AF XY: 0.0500 AC XY: 3717 AN XY: 74394

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0568

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.00349

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0253 Hom.: 73

Bravo AF: 0.0611

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505839; hg19: chr12-19660980;