chr10-3781714-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001300.6(KLF6):c.603G>A(p.Arg201=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00926 in 1,614,124 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0074 ( 8 hom., cov: 33)
Exomes 𝑓: 0.0095 ( 97 hom. )
Consequence
KLF6
NM_001300.6 synonymous
NM_001300.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.591
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 10-3781714-C-T is Benign according to our data. Variant chr10-3781714-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 132786.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.591 with no splicing effect.
BS2
?
High AC in GnomAd at 1125 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF6 | NM_001300.6 | c.603G>A | p.Arg201= | synonymous_variant | 2/4 | ENST00000497571.6 | |
KLF6 | NM_001160125.2 | c.603G>A | p.Arg201= | synonymous_variant | 2/3 | ||
KLF6 | NM_001160124.2 | c.550+53G>A | intron_variant | ||||
KLF6 | NR_027653.2 | n.717+81G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF6 | ENST00000497571.6 | c.603G>A | p.Arg201= | synonymous_variant | 2/4 | 1 | NM_001300.6 | P1 | |
KLF6 | ENST00000469435.1 | c.603G>A | p.Arg201= | synonymous_variant | 2/2 | 1 | |||
KLF6 | ENST00000542957.1 | c.603G>A | p.Arg201= | synonymous_variant | 2/3 | 5 | |||
KLF6 | ENST00000173785.4 | n.257+81G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00739 AC: 1125AN: 152190Hom.: 8 Cov.: 33
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GnomAD3 exomes AF: 0.00769 AC: 1930AN: 250900Hom.: 13 AF XY: 0.00783 AC XY: 1062AN XY: 135686
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GnomAD4 exome AF: 0.00946 AC: 13824AN: 1461816Hom.: 97 Cov.: 32 AF XY: 0.00942 AC XY: 6852AN XY: 727200
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GnomAD4 genome ? AF: 0.00739 AC: 1125AN: 152308Hom.: 8 Cov.: 33 AF XY: 0.00831 AC XY: 619AN XY: 74472
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | KLF6: BP4, BP7, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2018 | - - |
Hypotension Other:1
not provided, no classification provided | literature only | Centre for molecular medicine, Karolinska Institutet | - | - - |
Computational scores
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Name
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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