chr3-49173048-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_173546.3(KLHDC8B):c.279G>A(p.Pro93=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000515 in 1,609,774 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00054 ( 16 hom. )
Consequence
KLHDC8B
NM_173546.3 synonymous
NM_173546.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.04
Genes affected
KLHDC8B (HGNC:28557): (kelch domain containing 8B) This gene encodes a protein which forms a distinct beta-propeller protein structure of kelch domains allowing for protein-protein interactions. Mutations in this gene have been associated with Hodgkin lymphoma. [provided by RefSeq, Sep 2010]
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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=-0.74).
BP6
?
Variant 3-49173048-G-A is Benign according to our data. Variant chr3-49173048-G-A is described in ClinVar as [Benign]. Clinvar id is 2058265.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.04 with no splicing effect.
BS2
?
High AC in GnomAd at 46 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLHDC8B | NM_173546.3 | c.279G>A | p.Pro93= | synonymous_variant | 2/6 | ENST00000332780.4 | |
KLHDC8B | XM_006713015.4 | c.279G>A | p.Pro93= | synonymous_variant | 2/6 | ||
KLHDC8B | XM_006713016.4 | c.279G>A | p.Pro93= | synonymous_variant | 2/6 | ||
KLHDC8B | XM_005264938.4 | c.279G>A | p.Pro93= | synonymous_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLHDC8B | ENST00000332780.4 | c.279G>A | p.Pro93= | synonymous_variant | 2/6 | 1 | NM_173546.3 | P1 | |
KLHDC8B | ENST00000476495.2 | n.336G>A | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
KLHDC8B | ENST00000459846.6 | n.230+247G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 46AN: 152160Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00104 AC: 250AN: 240276Hom.: 8 AF XY: 0.00133 AC XY: 173AN XY: 130488
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GnomAD4 exome AF: 0.000537 AC: 783AN: 1457496Hom.: 16 Cov.: 31 AF XY: 0.000733 AC XY: 531AN XY: 724880
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 30, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at