rs7960653

Variant names:

• chr12-19589121-C-T
• rs7960653
• ENST00000512223.6:c.338+71008C>T

Variant summary

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

The ENST00000512223.6(AEBP2):​c.338+71008C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,026 control chromosomes in the GnomAD database, including 9,219 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 0.34 (9219 hom., cov: 33)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• Publications: 3 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]

LOC101928387 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928387	XR_007063236.1	n.471+28614C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.338+71008C>T		intron_variant	Intron 4 of 4	3		ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52127 AN: 151906 Hom.: 9219 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0874

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.343 AC: 52140 AN: 152026 Hom.: 9219 Cov.: 33 AF XY: 0.341 AC XY: 25319 AN XY: 74306

African (AFR) AF: 0.294 AC: 12200 AN: 41466

American (AMR) AF: 0.358 AC: 5469 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3468

East Asian (EAS) AF: 0.0872 AC: 451 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1324 AN: 4826

European-Finnish (FIN) AF: 0.386 AC: 4070 AN: 10536

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25794 AN: 67962

Other (OTH) AF: 0.344 AC: 726 AN: 2108

Alfa AF: 0.364 Hom.: 43621

Bravo AF: 0.337

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.78
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs7960653; hg19: chr12-19742055;