rs12592176

Variant summary

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

The NM_015995.4(KLF13):​c.578-17944G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,132 control chromosomes in the GnomAD database, including 14,627 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 0.42 ( 14627 hom., cov: 33)

Consequence

KLF13
NM_015995.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.25
Variant links:
Genes affected
KLF13 (HGNC:13672): (KLF transcription factor 13) KLF13 belongs to a family of transcription factors that contain 3 classical zinc finger DNA-binding domains consisting of a zinc atom tetrahedrally coordinated by 2 cysteines and 2 histidines (C2H2 motif). These transcription factors bind to GC-rich sequences and related GT and CACCC boxes (Scohy et al., 2000 [PubMed 11087666]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KLF13NM_015995.4 linkuse as main transcriptc.578-17944G>A intron_variant ENST00000307145.4
KLF13NM_001302461.2 linkuse as main transcriptc.577+26277G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KLF13ENST00000307145.4 linkuse as main transcriptc.578-17944G>A intron_variant 1 NM_015995.4 P1
KLF13ENST00000560473.1 linkuse as main transcriptc.13+14079G>A intron_variant 3
KLF13ENST00000558921.1 linkuse as main transcriptn.223+26277G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.424
AC:
64529
AN:
152016
Hom.:
14628
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.475
Gnomad AMR
AF:
0.398
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.563
Gnomad SAS
AF:
0.463
Gnomad FIN
AF:
0.477
Gnomad MID
AF:
0.443
Gnomad NFE
AF:
0.509
Gnomad OTH
AF:
0.432
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.424
AC:
64539
AN:
152132
Hom.:
14627
Cov.:
33
AF XY:
0.423
AC XY:
31430
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.253
Gnomad4 AMR
AF:
0.398
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.563
Gnomad4 SAS
AF:
0.461
Gnomad4 FIN
AF:
0.477
Gnomad4 NFE
AF:
0.508
Gnomad4 OTH
AF:
0.433
Alfa
AF:
0.458
Hom.:
2049
Bravo
AF:
0.413
Asia WGS
AF:
0.452
AC:
1576
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.11
DANN
Benign
0.38

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: rs12592176; hg19: chr15-31646269; API