chr14-54962541-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007086.4(WDHD1):c.2658G>A(p.Ser886=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,609,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00074 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
WDHD1
NM_007086.4 synonymous
NM_007086.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.33
Genes affected
WDHD1 (HGNC:23170): (WD repeat and HMG-box DNA binding protein 1) The protein encoded by this gene contains multiple N-terminal WD40 domains and a C-terminal high mobility group (HMG) box. WD40 domains are found in a variety of eukaryotic proteins and may function as adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. HMG boxes are found in many eukaryotic proteins involved in chromatin assembly, transcription and replication. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 14-54962541-C-T is Benign according to our data. Variant chr14-54962541-C-T is described in ClinVar as [Benign]. Clinvar id is 712596.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.34 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDHD1 | NM_007086.4 | c.2658G>A | p.Ser886= | synonymous_variant | 21/26 | ENST00000360586.8 | NP_009017.1 | |
WDHD1 | NM_001008396.3 | c.2289G>A | p.Ser763= | synonymous_variant | 20/25 | NP_001008397.1 | ||
WDHD1 | XM_006720012.2 | c.2658G>A | p.Ser886= | synonymous_variant | 21/26 | XP_006720075.1 | ||
WDHD1 | XM_011536373.3 | c.1569G>A | p.Ser523= | synonymous_variant | 12/17 | XP_011534675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDHD1 | ENST00000360586.8 | c.2658G>A | p.Ser886= | synonymous_variant | 21/26 | 1 | NM_007086.4 | ENSP00000353793 | P1 | |
WDHD1 | ENST00000420358.2 | c.2289G>A | p.Ser763= | synonymous_variant | 20/25 | 5 | ENSP00000399349 | |||
WDHD1 | ENST00000567693.1 | c.*1108G>A | 3_prime_UTR_variant, NMD_transcript_variant | 9/14 | 2 | ENSP00000456806 |
Frequencies
GnomAD3 genomes AF: 0.000730 AC: 111AN: 152114Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000465 AC: 116AN: 249392Hom.: 0 AF XY: 0.000378 AC XY: 51AN XY: 134918
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GnomAD4 exome AF: 0.000126 AC: 183AN: 1457352Hom.: 0 Cov.: 30 AF XY: 0.000110 AC XY: 80AN XY: 725268
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GnomAD4 genome AF: 0.000736 AC: 112AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.000806 AC XY: 60AN XY: 74416
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jul 04, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at