chr10-3779493-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001300.6(KLF6):c.*46A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
KLF6
NM_001300.6 3_prime_UTR
NM_001300.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.12
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF6 | NM_001300.6 | c.*46A>T | 3_prime_UTR_variant | 4/4 | ENST00000497571.6 | ||
KLF6 | NM_001160124.2 | c.*46A>T | 3_prime_UTR_variant | 4/4 | |||
KLF6 | NM_001160125.2 | c.*60A>T | 3_prime_UTR_variant | 3/3 | |||
KLF6 | NR_027653.2 | n.939A>T | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF6 | ENST00000497571.6 | c.*46A>T | 3_prime_UTR_variant | 4/4 | 1 | NM_001300.6 | P1 | ||
KLF6 | ENST00000542957.1 | c.*60A>T | 3_prime_UTR_variant | 3/3 | 5 | ||||
KLF6 | ENST00000173785.4 | n.479A>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
KLF6 | ENST00000461124.1 | n.210A>T | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 22
GnomAD4 exome
Cov.:
22
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
Bravo
AF:
ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
Hypotension Other:1
not provided, no classification provided | literature only | Centre for molecular medicine, Karolinska Institutet | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at