chr4-128871632-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_199320.4(JADE1):āc.1899A>Gā(p.Leu633=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00497 in 1,614,198 control chromosomes in the GnomAD database, including 224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.022 ( 111 hom., cov: 32)
Exomes š: 0.0032 ( 113 hom. )
Consequence
JADE1
NM_199320.4 synonymous
NM_199320.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0700
Genes affected
JADE1 (HGNC:30027): (jade family PHD finger 1) Enables transcription coactivator activity. Involved in histone acetylation and negative regulation of canonical Wnt signaling pathway. Acts upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Located in several cellular components, including ciliary basal body; cytosol; and nuclear speck. Part of histone acetyltransferase complex. [provided by Alliance of Genome Resources, Apr 2022]
SCLT1 (HGNC:26406): (sodium channel and clathrin linker 1) This gene encodes an adaptor protein. Studies of a related gene in rat suggest that the encoded protein functions to link clathrin to the sodium channel protein type 10 subunit alpha protein. The encoded protein has also been identified as a component of distal appendages of centrioles that is necessary for ciliogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 4-128871632-A-G is Benign according to our data. Variant chr4-128871632-A-G is described in ClinVar as [Benign]. Clinvar id is 776018.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.07 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0715 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JADE1 | NM_199320.4 | c.1899A>G | p.Leu633= | synonymous_variant | 11/11 | ENST00000226319.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JADE1 | ENST00000226319.11 | c.1899A>G | p.Leu633= | synonymous_variant | 11/11 | 5 | NM_199320.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0223 AC: 3388AN: 152206Hom.: 110 Cov.: 32
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GnomAD3 exomes AF: 0.00655 AC: 1643AN: 250830Hom.: 53 AF XY: 0.00527 AC XY: 714AN XY: 135540
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GnomAD4 exome AF: 0.00316 AC: 4614AN: 1461874Hom.: 113 Cov.: 32 AF XY: 0.00303 AC XY: 2207AN XY: 727238
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GnomAD4 genome AF: 0.0224 AC: 3405AN: 152324Hom.: 111 Cov.: 32 AF XY: 0.0220 AC XY: 1637AN XY: 74490
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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 | Jun 27, 2018 | - - |
Computational scores
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Benign
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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