dbSNP rs10795076: KLF6:c.103-937C>A (chr10-3783151-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001300.6(KLF6):c.103-937C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,986 control chromosomes in the GnomAD database, including 1,784 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 0.15 ( 1783 hom., cov: 32)

Exomes 𝑓: 0.18 ( 1 hom. )

Consequence

KLF6
NM_001300.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

Publications

5 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KLF6	NM_001300.6	MANE Select	c.103-937C>A	intron	N/A	NP_001291.3
KLF6	NM_001160124.2		c.103-937C>A	intron	N/A	NP_001153596.1
KLF6	NM_001160125.2		c.103-937C>A	intron	N/A	NP_001153597.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
KLF6	ENST00000497571.6	TSL:1 MANE Select	c.103-937C>A	intron	N/A	ENSP00000419923.1
KLF6	ENST00000469435.1	TSL:1	c.103-937C>A	intron	N/A	ENSP00000419079.1
KLF6	ENST00000542957.1	TSL:5	c.103-937C>A	intron	N/A	ENSP00000445301.1

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22787

AN:

151790

Hom.:

1780

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.179

AC:

AN:

Hom.:

AF XY:

0.117

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.167

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.150

AC:

22800

AN:

151908

Hom.:

1783

Cov.:

AF XY:

0.152

AC XY:

11250

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.107

AC:

4429

AN:

41390

American (AMR)

AF:

0.226

AC:

3446

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

510

AN:

3470

East Asian (EAS)

AF:

0.163

AC:

842

AN:

5166

South Asian (SAS)

AF:

0.220

AC:

1060

AN:

4810

European-Finnish (FIN)

AF:

0.131

AC:

1380

AN:

10532

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.156

AC:

10633

AN:

67956

Other (OTH)

AF:

0.165

AC:

348

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

987

1973

2960

3946

4933

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.156

Hom.:

6398

Bravo

AF:

0.154

Asia WGS

AF:

0.199

AC:

694

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over