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rs11044734

chr12-19642972-G-Cchr12-19642972-G-T

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0380
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]

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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 = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC101928387XR_007063236.1 linkuse as main transcriptn.472-7424G>C intron_variant, non_coding_transcript_variant
LOC101928387XR_001749035.2 linkuse as main transcriptn.526-7424G>C intron_variant, non_coding_transcript_variant
LOC101928387XR_001749036.2 linkuse as main transcriptn.526-6726G>C intron_variant, non_coding_transcript_variant
LOC101928387XR_007063237.1 linkuse as main transcriptn.928-7424G>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AEBP2ENST00000512223.6 linkuse as main transcriptc.339-77661G>C intron_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0833
AC:
12515
AN:
150234
Hom.:
666
Cov.:
29
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0832
AC:
12516
AN:
150356
Hom.:
667
Cov.:
29
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.:
83
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.

Other links and lift over

dbSNP: rs11044734; hg19: chr12-19795906; API