Variant chr13-74065662-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_007249.5(KLF12):c.-32+68077A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,826 control chromosomes in the GnomAD database, including 25,812 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 0.55 ( 25812 hom., cov: 29)

Consequence

KLF12
NM_007249.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

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]

KLF12 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 (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
KLF12	NM_001400136.1 link	c.-32+68310A>G	intron_variant	NP_001387065.1
KLF12	NM_001400139.1 link	c.-31-70609A>G	intron_variant	NP_001387068.1
KLF12	NM_007249.5 link	c.-32+68077A>G	intron_variant	NP_009180.3	Q9Y4X4-1Q8WWI3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF12	ENST00000377669.7 link	c.-32+68077A>G		intron_variant		1		ENSP00000366897.2		Q9Y4X4-1
KLF12	ENST00000703967.1 link	c.-32+68310A>G		intron_variant				ENSP00000515592.1		Q9Y4X4-1

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

83823

AN:

151708

Hom.:

25821

Cov.:

show subpopulations

Gnomad AFR

AF:

0.267

Gnomad AMI

AF:

0.632

Gnomad AMR

AF:

0.531

Gnomad ASJ

AF:

0.643

Gnomad EAS

AF:

0.872

Gnomad SAS

AF:

0.798

Gnomad FIN

AF:

0.690

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.661

Gnomad OTH

AF:

0.577

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

GnomAD4 genome

AF:

0.552

AC:

83822

AN:

151826

Hom.:

25812

Cov.:

AF XY:

0.559

AC XY:

41439

AN XY:

74178

show subpopulations

Gnomad4 AFR

AF:

0.267

Gnomad4 AMR

AF:

0.530

Gnomad4 ASJ

AF:

0.643

Gnomad4 EAS

AF:

0.872

Gnomad4 SAS

AF:

0.799

Gnomad4 FIN

AF:

0.690

Gnomad4 NFE

AF:

0.661

Gnomad4 OTH

AF:

0.576

Alfa

AF:

0.582

Hom.:

4479

Bravo

AF:

0.526

Asia WGS

AF:

0.748

AC:

2604

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

2.8

DANN

Benign

0.61

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