rs10841287

Variant names:

• chr12-19626859-T-C
• rs10841287
• ENST00000512223.6:c.339-93774T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-19626859-T-C
• chr12-19626859-T-G

Variant summary

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

The ENST00000512223.6(AEBP2):​c.339-93774T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,016 control chromosomes in the GnomAD database, including 9,679 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 0.31 (9679 hom., cov: 32)
• Consequence: AEBP2 ENST00000512223.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928387	XR_001749035.2	n.526-23537T>C		intron_variant	Intron 1 of 3
LOC101928387	XR_001749036.2	n.526-22839T>C		intron_variant	Intron 1 of 4
LOC101928387	XR_007063236.1	n.472-23537T>C		intron_variant	Intron 3 of 6
LOC101928387	XR_007063237.1	n.927+6373T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-93774T>C		intron_variant	Intron 4 of 4	3		ENSP00000445587.1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47731 AN: 151898 Hom.: 9653 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.314 AC: 47797 AN: 152016 Hom.: 9679 Cov.: 32 AF XY: 0.310 AC XY: 23033 AN XY: 74302

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.261

Alfa AF: 0.209 Hom.: 5795

Bravo AF: 0.322

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10841287; hg19: chr12-19779793;