chr19-18668030-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_018316.3(KLHL26):c.633C>T(p.Phe211=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00048 in 1,609,032 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 33)
Exomes 𝑓: 0.00028 ( 3 hom. )
Consequence
KLHL26
NM_018316.3 synonymous
NM_018316.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.10
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 19-18668030-C-T is Benign according to our data. Variant chr19-18668030-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2649589.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.1 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHL26 | NM_018316.3 | c.633C>T | p.Phe211= | synonymous_variant | 3/3 | ENST00000300976.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHL26 | ENST00000300976.9 | c.633C>T | p.Phe211= | synonymous_variant | 3/3 | 1 | NM_018316.3 | P1 | |
KLHL26 | ENST00000599006.5 | c.405+228C>T | intron_variant | 5 | |||||
KLHL26 | ENST00000596843.1 | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00234 AC: 357AN: 152248Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.000684 AC: 167AN: 244272Hom.: 1 AF XY: 0.000437 AC XY: 58AN XY: 132800
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GnomAD4 exome AF: 0.000283 AC: 412AN: 1456666Hom.: 3 Cov.: 34 AF XY: 0.000262 AC XY: 190AN XY: 724860
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GnomAD4 genome ? AF: 0.00236 AC: 360AN: 152366Hom.: 2 Cov.: 33 AF XY: 0.00231 AC XY: 172AN XY: 74508
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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 | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | KLHL26: BP4, BP7, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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