rs7960653

chr12-19589121-C-T

Variant summary

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

The XR_007063236.1(LOC101928387):n.471+28614C>T variant causes a intron, non coding transcript 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: LOC101928387 XR_007063236.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30

Genes affected

LOC101928387 (HGNC:):

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=-0.93).
• 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/exons	MANE	UniProt
LOC101928387	XR_007063236.1	n.471+28614C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AEBP2	ENST00000512223.6	c.338+71008C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.0872

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.344

Alfa AF: 0.369 Hom.: 21696

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7960653; hg19: chr12-19742055;