chr21-33559867-CTCT-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000356577.10(SON):c.6657+97_6657+99del variant causes a intron change. The variant allele was found at a frequency of 0.000000689 in 1,450,686 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
SON
ENST00000356577.10 intron
ENST00000356577.10 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.64
Genes affected
SON (HGNC:11183): (SON DNA and RNA binding protein) This gene encodes a protein that contains multiple simple repeats. The encoded protein binds RNA and promotes pre-mRNA splicing, particularly of transcripts with poor splice sites. The protein also recognizes a specific DNA sequence found in the human hepatitis B virus (HBV) and represses HBV core promoter activity. There is a pseudogene for this gene on chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 21-33559867-CTCT-C is Benign according to our data. Variant chr21-33559867-CTCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 2105909.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SON | NM_138927.4 | c.6657+97_6657+99del | intron_variant | ENST00000356577.10 | NP_620305.3 | |||
SON | NM_001291412.3 | c.741+97_741+99del | intron_variant | NP_001278341.1 | ||||
SON | NM_032195.3 | c.6658-5_6658-3del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NP_115571.3 | ||||
SON | NR_103797.2 | n.6712+97_6712+99del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SON | ENST00000356577.10 | c.6657+97_6657+99del | intron_variant | 1 | NM_138927.4 | ENSP00000348984 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 244804Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132524
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GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450686Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 720202
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GnomAD4 genome Cov.: 32
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Mar 17, 2022 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at