Variant 12-19648661-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007063236.1(LOC101928387):n.472-1735G>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 0.84 in 152,170 control chromosomes in the GnomAD database, including 54,240 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 0.84 ( 54240 hom., cov: 32)

Consequence

LOC101928387
XR_007063236.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0780

Variant links:

Genes affected

LOC101928387 (HGNC:):

LOC101928387 links:

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]

AEBP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC101928387	XR_007063236.1 linkuse as main transcript	n.472-1735G>T	intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749035.2 linkuse as main transcript	n.526-1735G>T	intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749036.2 linkuse as main transcript	n.526-1037G>T	intron_variant, non_coding_transcript_variant
LOC101928387	XR_007063237.1 linkuse as main transcript	n.928-1735G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AEBP2	ENST00000512223.6 linkuse as main transcript	c.339-71972G>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127741

AN:

152052

Hom.:

54191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.919

Gnomad AMI

AF:

0.853

Gnomad AMR

AF:

0.799

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.578

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.801

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.842

Gnomad OTH

AF:

0.847

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

GnomAD4 genome

AF:

0.840

AC:

127844

AN:

152170

Hom.:

54240

Cov.:

AF XY:

0.831

AC XY:

61802

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.919

Gnomad4 AMR

AF:

0.799

Gnomad4 ASJ

AF:

0.877

Gnomad4 EAS

AF:

0.578

Gnomad4 SAS

AF:

0.595

Gnomad4 FIN

AF:

0.801

Gnomad4 NFE

AF:

0.842

Gnomad4 OTH

AF:

0.848

Alfa

AF:

0.836

Hom.:

70302

Bravo

AF:

0.843

Asia WGS

AF:

0.625

AC:

2175

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.32

DANN

Benign

0.28

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over