rs4885065

Variant names:

• chr13-73075497-G-A
• rs4885065
• NM_001730.5:c.1196-211G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-73075497-G-A
• chr13-73075497-G-T
• chr13-73075497-G-C

Variant summary

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

The NM_001730.5(KLF5):​c.1196-211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,126 control chromosomes in the GnomAD database, including 50,029 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.81 (50029 hom., cov: 31)
• Consequence: KLF5 NM_001730.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001730.5. 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
	KLF5	NM_001730.5	MANE Select	c.1196-211G>A		intron	N/A	NP_001721.2
	KLF5	NM_001286818.2		c.923-211G>A		intron	N/A	NP_001273747.1	Q13887-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF5	ENST00000377687.6	TSL:1 MANE Select	c.1196-211G>A		intron	N/A	ENSP00000366915.4	Q13887-1
	KLF5	ENST00000539231.5	TSL:1	c.923-211G>A		intron	N/A	ENSP00000440407.1	Q13887-4
	KLF5	ENST00000851191.1		c.1136-211G>A		intron	N/A	ENSP00000521250.1

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123047 AN: 152008 Hom.: 50001 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.809 AC: 123127 AN: 152126 Hom.: 50029 Cov.: 31 AF XY: 0.811 AC XY: 60356 AN XY: 74394

African (AFR) AF: 0.718 AC: 29763 AN: 41460

American (AMR) AF: 0.865 AC: 13223 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2966 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4451 AN: 5182

South Asian (SAS) AF: 0.841 AC: 4059 AN: 4828

European-Finnish (FIN) AF: 0.863 AC: 9133 AN: 10582

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.835 AC: 56765 AN: 68002

Other (OTH) AF: 0.813 AC: 1716 AN: 2112

Alfa AF: 0.828 Hom.: 102760

Bravo AF: 0.806

Asia WGS AF: 0.845 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.55
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4885065; hg19: chr13-73649635;