Variant rs17731 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001300.6(KLF6):c.*170C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 697,650 control chromosomes in the GnomAD database, including 43,348 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 0.27 ( 7164 hom., cov: 32)

Exomes 𝑓: 0.35 ( 36184 hom. )

Consequence

KLF6
NM_001300.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.35

Variant links:

Genes affected

KLF6 (HGNC:2235): (KLF transcription factor 6) This gene encodes a member of the Kruppel-like family of transcription factors. The zinc finger protein is a transcriptional activator, and functions as a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene, some of which are implicated in carcinogenesis. [provided by RefSeq, May 2009]

KLF6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
KLF6	NM_001300.6 linkuse as main transcript	c.*170C>T	3_prime_UTR_variant	4/4	ENST00000497571.6	NP_001291.3
KLF6	NM_001160124.2 linkuse as main transcript	c.*170C>T	3_prime_UTR_variant	4/4		NP_001153596.1
KLF6	NM_001160125.2 linkuse as main transcript	c.*184C>T	3_prime_UTR_variant	3/3		NP_001153597.1
KLF6	NR_027653.2 linkuse as main transcript	n.1063C>T	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF6	ENST00000497571.6 linkuse as main transcript	c.*170C>T	3_prime_UTR_variant	4/4	1	NM_001300.6	ENSP00000419923	P1	Q99612-1
KLF6	ENST00000542957.1 linkuse as main transcript	c.*184C>T	3_prime_UTR_variant	3/3	5		ENSP00000445301		Q99612-3
KLF6	ENST00000173785.4 linkuse as main transcript	n.603C>T	non_coding_transcript_exon_variant	3/3	2
KLF6	ENST00000461124.1 linkuse as main transcript	n.334C>T	non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41682

AN:

151972

Hom.:

7169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.501

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.282

GnomAD3 exomes

AF:

0.334

AC:

46496

AN:

139352

Hom.:

8397

AF XY:

0.341

AC XY:

25784

AN XY:

75544

show subpopulations

Gnomad AFR exome

AF:

0.0628

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.336

Gnomad EAS exome

AF:

0.476

Gnomad SAS exome

AF:

0.344

Gnomad FIN exome

AF:

0.259

Gnomad NFE exome

AF:

0.374

Gnomad OTH exome

AF:

0.349

GnomAD4 exome

AF:

0.355

AC:

193428

AN:

545560

Hom.:

36184

Cov.:

AF XY:

0.358

AC XY:

105563

AN XY:

294840

show subpopulations

Gnomad4 AFR exome

AF:

0.0697

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.516

Gnomad4 SAS exome

AF:

0.351

Gnomad4 FIN exome

AF:

0.266

Gnomad4 NFE exome

AF:

0.377

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.274

AC:

41666

AN:

152090

Hom.:

7164

Cov.:

AF XY:

0.270

AC XY:

20054

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.0728

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.501

Gnomad4 SAS

AF:

0.334

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.375

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.315

Hom.:

4371

Bravo

AF:

0.266

Asia WGS

AF:

0.327

AC:

1135

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over