chr13-73055921-G-C

Position:

• chr13-73055921-G-C

Variant summary

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

The ENST00000539231.5(KLF5):​c.-13+763G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,972 control chromosomes in the GnomAD database, including 18,792 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 0.48 (18792 hom., cov: 32)
• Consequence: KLF5 ENST00000539231.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

Genes affected

KLF5 (HGNC:6349): (KLF transcription factor 5) This gene encodes a member of the Kruppel-like factor subfamily of zinc finger proteins. The encoded protein is a transcriptional activator that binds directly to a specific recognition motif in the promoters of target genes. This protein acts downstream of multiple different signaling pathways and is regulated by post-translational modification. It may participate in both promoting and suppressing cell proliferation. Expression of this gene may be changed in a variety of different cancers and in cardiovascular disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF5	NM_001286818.2	c.-13+763G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF5	ENST00000539231.5	c.-13+763G>C		intron_variant		1		A1
KLF5	ENST00000477333.5	n.183+763G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72825 AN: 151854 Hom.: 18779 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.479 AC: 72870 AN: 151972 Hom.: 18792 Cov.: 32 AF XY: 0.477 AC XY: 35432 AN XY: 74266

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.490

Alfa AF: 0.425 Hom.: 1311

Bravo AF: 0.454

Asia WGS AF: 0.297 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11841945; hg19: chr13-73630059; COSMIC: COSV66614701; COSMIC: COSV66614701;