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rs11044737

chr12-19648819-G-A

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
LOC101928387XR_007063236.1 linkuse as main transcriptn.472-1577G>A intron_variant, non_coding_transcript_variant
LOC101928387XR_001749035.2 linkuse as main transcriptn.526-1577G>A intron_variant, non_coding_transcript_variant
LOC101928387XR_001749036.2 linkuse as main transcriptn.526-879G>A intron_variant, non_coding_transcript_variant
LOC101928387XR_007063237.1 linkuse as main transcriptn.928-1577G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AEBP2ENST00000512223.6 linkuse as main transcriptc.339-71814G>A intron_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0969
AC:
14727
AN:
151980
Hom.:
807
Cov.:
31
show subpopulations
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0969
AC:
14733
AN:
152098
Hom.:
809
Cov.:
31
AF XY:
0.0972
AC XY:
7225
AN XY:
74332
show subpopulations
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

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

Other links and lift over

dbSNP: rs11044737; hg19: chr12-19801753; API