Variant chr8-102650125-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_005655.4(KLF10):c.*7G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0249 in 1,613,606 control chromosomes in the GnomAD database, including 631 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.019 ( 35 hom., cov: 33)

Exomes 𝑓: 0.026 ( 596 hom. )

Consequence

KLF10
NM_005655.4 3_prime_UTR

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.46

Variant links:

Genes affected

KLF10 (HGNC:11810): (KLF transcription factor 10) This gene encodes a member of a family of proteins that feature C2H2-type zinc finger domains. The encoded protein is a transcriptional repressor that acts as an effector of transforming growth factor beta signaling. Activity of this protein may inhibit the growth of cancers, particularly pancreatic cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]

KLF10 links:

KLF10 (HGNC:):

KLF10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 8-102650125-C-T is Benign according to our data. Variant chr8-102650125-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1704092.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0187 (2852/152324) while in subpopulation SAS AF= 0.0431 (208/4828). AF 95% confidence interval is 0.0383. There are 35 homozygotes in gnomad4. There are 1473 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 35 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
KLF10	NM_005655.4 linkuse as main transcript	c.*7G>A	3_prime_UTR_variant	4/4	ENST00000285407.11	NP_005646.1	Q13118-1
KLF10	NM_001032282.4 linkuse as main transcript	c.*7G>A	3_prime_UTR_variant	4/4		NP_001027453.1	Q13118-2
KLF10	NR_103759.2 linkuse as main transcript	n.775G>A	non_coding_transcript_exon_variant	3/3
KLF10	NR_103760.2 linkuse as main transcript	n.898G>A	non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF10	ENST00000285407.11 linkuse as main transcript	c.*7G>A		3_prime_UTR_variant	4/4	1	NM_005655.4	ENSP00000285407.6		Q13118-1
KLF10	ENST00000395884.3 linkuse as main transcript	c.*7G>A		3_prime_UTR_variant	4/4	1		ENSP00000379222.3		Q13118-2

Frequencies

GnomAD3 genomes

AF:

0.0187

AC:

2851

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00422

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0217

Gnomad ASJ

AF:

0.0257

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0428

Gnomad FIN

AF:

0.0276

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0249

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.0238

AC:

5959

AN:

250504

Hom.:

110

AF XY:

0.0255

AC XY:

3452

AN XY:

135274

show subpopulations

Gnomad AFR exome

AF:

0.00345

Gnomad AMR exome

AF:

0.0179

Gnomad ASJ exome

AF:

0.0283

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0430

Gnomad FIN exome

AF:

0.0303

Gnomad NFE exome

AF:

0.0253

Gnomad OTH exome

AF:

0.0275

GnomAD4 exome

AF:

0.0255

AC:

37305

AN:

1461282

Hom.:

596

Cov.:

AF XY:

0.0260

AC XY:

18920

AN XY:

726848

show subpopulations

Gnomad4 AFR exome

AF:

0.00293

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.0274

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0421

Gnomad4 FIN exome

AF:

0.0303

Gnomad4 NFE exome

AF:

0.0259

Gnomad4 OTH exome

AF:

0.0239

GnomAD4 genome

AF:

0.0187

AC:

2852

AN:

152324

Hom.:

Cov.:

AF XY:

0.0198

AC XY:

1473

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00421

Gnomad4 AMR

AF:

0.0218

Gnomad4 ASJ

AF:

0.0257

Gnomad4 EAS

AF:

0.000964

Gnomad4 SAS

AF:

0.0431

Gnomad4 FIN

AF:

0.0276

Gnomad4 NFE

AF:

0.0249

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.0220

Hom.:

Bravo

AF:

0.0169

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 08, 2022

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.021

DANN

Benign

0.59

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over