rs12592176

Positions:

• chr15-31354066-G-A
• chr15-31354066-G-C
• chr15-31354066-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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]

ACMG classification

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
KLF13	NM_015995.4	c.578-17944G>A		intron_variant		ENST00000307145.4
KLF13	NM_001302461.2	c.577+26277G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF13	ENST00000307145.4	c.578-17944G>A		intron_variant		1	NM_015995.4	P1
KLF13	ENST00000560473.1	c.13+14079G>A		intron_variant		3
KLF13	ENST00000558921.1	n.223+26277G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64529 AN: 152016 Hom.: 14628 Cov.: 33

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

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

Other links and lift over

dbSNP: rs12592176; hg19: chr15-31646269;