rs10795076

Positions:

• chr10-3783151-G-T

Variant summary

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

The ENST00000497571.6(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 ENST00000497571.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF6	NM_001300.6	c.103-937C>A		intron_variant		ENST00000497571.6	NP_001291.3
KLF6	NM_001160124.2	c.103-937C>A		intron_variant			NP_001153596.1
KLF6	NM_001160125.2	c.103-937C>A		intron_variant			NP_001153597.1
KLF6	NR_027653.2	n.298-937C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF6	ENST00000497571.6	c.103-937C>A		intron_variant		1	NM_001300.6	ENSP00000419923	P1
KLF6	ENST00000469435.1	c.103-937C>A		intron_variant		1		ENSP00000419079
KLF6	ENST00000542957.1	c.103-937C>A		intron_variant		5		ENSP00000445301
KLF6	ENST00000380946.3	n.337+65C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22787 AN: 151790 Hom.: 1780 Cov.: 32

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: 14 AN: 78 Hom.: 1 AF XY: 0.117 AC XY: 7 AN XY: 60

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.150 AC: 22800 AN: 151908 Hom.: 1783 Cov.: 32 AF XY: 0.152 AC XY: 11250 AN XY: 74236

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.165

Alfa AF: 0.160 Hom.: 2875

Bravo AF: 0.154

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.65
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs10795076; hg19: chr10-3825343;