13-73859670-T-G

Variant summary

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

The NM_007249.5(KLF12):​c.124-13297A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,026 control chromosomes in the GnomAD database, including 34,634 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 0.67 ( 34634 hom., cov: 32)

Consequence

KLF12
NM_007249.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.760
Variant links:
Genes affected
KLF12 (HGNC:6346): (KLF transcription factor 12) Activator protein-2 alpha (AP-2 alpha) is a developmentally-regulated transcription factor and important regulator of gene expression during vertebrate development and carcinogenesis. The protein encoded by this gene is a member of the Kruppel-like zinc finger protein family and can repress expression of the AP-2 alpha gene by binding to a specific site in the AP-2 alpha gene promoter. Repression by the encoded protein requires binding with a corepressor, CtBP1. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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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 (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KLF12NM_001400136.1 linkc.124-13297A>C intron_variant NP_001387065.1
KLF12NM_001400139.1 linkc.124-13297A>C intron_variant NP_001387068.1
KLF12NM_001400141.1 linkc.124-13297A>C intron_variant NP_001387070.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KLF12ENST00000377669.7 linkc.124-13297A>C intron_variant 1 ENSP00000366897.2 Q9Y4X4-1
KLF12ENST00000703967.1 linkc.124-13297A>C intron_variant ENSP00000515592.1 Q9Y4X4-1
KLF12ENST00000472022.1 linkn.158-13297A>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.668
AC:
101521
AN:
151908
Hom.:
34616
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.534
Gnomad AMI
AF:
0.733
Gnomad AMR
AF:
0.667
Gnomad ASJ
AF:
0.653
Gnomad EAS
AF:
0.712
Gnomad SAS
AF:
0.657
Gnomad FIN
AF:
0.765
Gnomad MID
AF:
0.658
Gnomad NFE
AF:
0.733
Gnomad OTH
AF:
0.656
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.668
AC:
101581
AN:
152026
Hom.:
34634
Cov.:
32
AF XY:
0.671
AC XY:
49873
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.534
Gnomad4 AMR
AF:
0.667
Gnomad4 ASJ
AF:
0.653
Gnomad4 EAS
AF:
0.713
Gnomad4 SAS
AF:
0.658
Gnomad4 FIN
AF:
0.765
Gnomad4 NFE
AF:
0.733
Gnomad4 OTH
AF:
0.646
Alfa
AF:
0.712
Hom.:
42630
Bravo
AF:
0.654
Asia WGS
AF:
0.650
AC:
2256
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.25
DANN
Benign
0.78

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs4883955; hg19: chr13-74433807; API