rs8033248

Positions:

• chr15-31380377-C-T

Variant summary

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

The NM_001302461.2(KLF13):​c.577+52588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,076 control chromosomes in the GnomAD database, including 13,106 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 0.41 (13106 hom., cov: 33)
• Consequence: KLF13 NM_001302461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

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=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF13	NM_001302461.2	c.577+52588C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF13	ENST00000558921.1	n.223+52588C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62958 AN: 151956 Hom.: 13105 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.414 AC: 62970 AN: 152076 Hom.: 13106 Cov.: 33 AF XY: 0.416 AC XY: 30903 AN XY: 74338

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.383

Alfa AF: 0.415 Hom.: 7278

Bravo AF: 0.414

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.3
DANN	Benign	0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8033248; hg19: chr15-31672580;