rs17731
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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
NM_001300.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.35
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]
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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 | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF6 | NM_001300.6 | c.*170C>T | 3_prime_UTR_variant | 4/4 | ENST00000497571.6 | ||
KLF6 | NM_001160124.2 | c.*170C>T | 3_prime_UTR_variant | 4/4 | |||
KLF6 | NM_001160125.2 | c.*184C>T | 3_prime_UTR_variant | 3/3 | |||
KLF6 | NR_027653.2 | n.1063C>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF6 | ENST00000497571.6 | c.*170C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_001300.6 | P1 | ||
KLF6 | ENST00000542957.1 | c.*184C>T | 3_prime_UTR_variant | 3/3 | 5 | ||||
KLF6 | ENST00000173785.4 | n.603C>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
KLF6 | ENST00000461124.1 | n.334C>T | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.274 AC: 41682AN: 151972Hom.: 7169 Cov.: 32
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GnomAD3 exomes AF: 0.334 AC: 46496AN: 139352Hom.: 8397 AF XY: 0.341 AC XY: 25784AN XY: 75544
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GnomAD4 exome AF: 0.355 AC: 193428AN: 545560Hom.: 36184 Cov.: 5 AF XY: 0.358 AC XY: 105563AN XY: 294840
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GnomAD4 genome ? AF: 0.274 AC: 41666AN: 152090Hom.: 7164 Cov.: 32 AF XY: 0.270 AC XY: 20054AN XY: 74352
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at