Variant rs11044734 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.472-7424G>C 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 0.0832 in 150,356 control chromosomes in the GnomAD database, including 667 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 0.083 ( 667 hom., cov: 29)

Consequence

LOC101928387
XR_007063236.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0380

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC101928387	XR_007063236.1 linkuse as main transcript	n.472-7424G>C	intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749035.2 linkuse as main transcript	n.526-7424G>C	intron_variant, non_coding_transcript_variant
LOC101928387	XR_001749036.2 linkuse as main transcript	n.526-6726G>C	intron_variant, non_coding_transcript_variant
LOC101928387	XR_007063237.1 linkuse as main transcript	n.928-7424G>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AEBP2	ENST00000512223.6 linkuse as main transcript	c.339-77661G>C		intron_variant		3		ENSP00000445587

Frequencies

GnomAD3 genomes

AF:

0.0833

AC:

12515

AN:

150234

Hom.:

666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0392

Gnomad AMI

AF:

0.0585

Gnomad AMR

AF:

0.0630

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.252

Gnomad SAS

AF:

0.0647

Gnomad FIN

AF:

0.0988

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.0974

Gnomad OTH

AF:

0.0739

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

GnomAD4 genome

AF:

0.0832

AC:

12516

AN:

150356

Hom.:

667

Cov.:

AF XY:

0.0835

AC XY:

6119

AN XY:

73322

show subpopulations

Gnomad4 AFR

AF:

0.0393

Gnomad4 AMR

AF:

0.0628

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.252

Gnomad4 SAS

AF:

0.0652

Gnomad4 FIN

AF:

0.0988

Gnomad4 NFE

AF:

0.0974

Gnomad4 OTH

AF:

0.0736

Alfa

AF:

0.0788

Hom.:

Bravo

AF:

0.0797

Asia WGS

AF:

0.126

AC:

439

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

2.6

DANN

Benign

0.81

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