12-19446067-A-G

Variant names:

• chr12-19446067-A-G
• rs11616166
• NM_153207.5:c.671+5697A>G

Variant summary

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

The NM_153207.5(AEBP2):​c.671+5697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 151,038 control chromosomes in the GnomAD database, including 419 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 0.067 (419 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: AEBP2 NM_153207.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 2 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]

RNU6-254P (HGNC:47217): (RNA, U6 small nuclear 254, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AEBP2	NM_153207.5	c.671+5697A>G		intron_variant	Intron 1 of 7	ENST00000266508.14	NP_694939.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000266508.14	c.671+5697A>G		intron_variant	Intron 1 of 7	1	NM_153207.5	ENSP00000266508.9

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10042 AN: 150916 Hom.: 418 Cov.: 33

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0492

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0606

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0665 AC: 10049 AN: 151038 Hom.: 419 Cov.: 33 AF XY: 0.0683 AC XY: 5036 AN XY: 73754

African (AFR) AF: 0.0331 AC: 1366 AN: 41298

American (AMR) AF: 0.0661 AC: 999 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.0492 AC: 170 AN: 3458

East Asian (EAS) AF: 0.165 AC: 843 AN: 5110

South Asian (SAS) AF: 0.190 AC: 905 AN: 4758

European-Finnish (FIN) AF: 0.0601 AC: 625 AN: 10406

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 4984 AN: 67638

Other (OTH) AF: 0.0652 AC: 134 AN: 2054

Alfa AF: 0.0688 Hom.: 74

Bravo AF: 0.0605

Asia WGS AF: 0.178 AC: 618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11616166; hg19: chr12-19599001;