rs11855557

Variant names:

• chr15-31378522-G-A
• rs11855557
• NM_001302461.2:c.577+50733G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-31378522-G-A
• chr15-31378522-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302461.2(KLF13):​c.577+50733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,934 control chromosomes in the GnomAD database, including 27,653 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 0.60 (27653 hom., cov: 31)
• Consequence: KLF13 NM_001302461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 2 publications found

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]

KLF13 Gene-Disease associations (from GenCC):

• congenital heart disease

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302461.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF13	NM_001302461.2		c.577+50733G>A		intron	N/A	NP_001289390.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF13	ENST00000558921.1	TSL:3	n.223+50733G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90721 AN: 151816 Hom.: 27592 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.598 AC: 90841 AN: 151934 Hom.: 27653 Cov.: 31 AF XY: 0.596 AC XY: 44251 AN XY: 74224

African (AFR) AF: 0.708 AC: 29338 AN: 41440

American (AMR) AF: 0.597 AC: 9122 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3234 AN: 5140

South Asian (SAS) AF: 0.488 AC: 2348 AN: 4808

European-Finnish (FIN) AF: 0.555 AC: 5852 AN: 10546

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37283 AN: 67954

Other (OTH) AF: 0.609 AC: 1281 AN: 2102

Alfa AF: 0.558 Hom.: 3526

Bravo AF: 0.609

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11855557; hg19: chr15-31670725;