rs11044737

Positions:

• chr12-19648819-G-A

Variant summary

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

The XR_007063236.1(LOC101928387):​n.472-1577G>A 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 0.0969 in 152,098 control chromosomes in the GnomAD database, including 809 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 0.097 (809 hom., cov: 31)
• Consequence: LOC101928387 XR_007063236.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101928387	XR_007063236.1	n.472-1577G>A		intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749035.2	n.526-1577G>A		intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749036.2	n.526-879G>A		intron_variant, non_coding_transcript_variant
LOC101928387	XR_007063237.1	n.928-1577G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6	c.339-71814G>A		intron_variant		3		ENSP00000445587

Frequencies

GnomAD3 genomes AF: 0.0969 AC: 14727 AN: 151980 Hom.: 807 Cov.: 31

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0969 AC: 14733 AN: 152098 Hom.: 809 Cov.: 31 AF XY: 0.0972 AC XY: 7225 AN XY: 74332

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.0665

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0969

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0980 Hom.: 1605

Bravo AF: 0.0952

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11044737; hg19: chr12-19801753;