rs754718251
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_018013.4(SOBP):āc.1530G>Cā(p.Gly510=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000354 in 1,594,552 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 Likely benign (ā ā ).
Frequency
Genomes: š 0.00024 ( 0 hom., cov: 31)
Exomes š: 0.00037 ( 0 hom. )
Consequence
SOBP
NM_018013.4 synonymous
NM_018013.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.788
Genes affected
SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 6-107634374-G-C is Benign according to our data. Variant chr6-107634374-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 436827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.788 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOBP | NM_018013.4 | c.1530G>C | p.Gly510= | synonymous_variant | 6/7 | ENST00000317357.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOBP | ENST00000317357.10 | c.1530G>C | p.Gly510= | synonymous_variant | 6/7 | 5 | NM_018013.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152046Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000182 AC: 40AN: 219808Hom.: 0 AF XY: 0.000124 AC XY: 15AN XY: 121360
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GnomAD4 exome AF: 0.000366 AC: 528AN: 1442506Hom.: 0 Cov.: 34 AF XY: 0.000365 AC XY: 262AN XY: 717494
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GnomAD4 genome ? AF: 0.000243 AC: 37AN: 152046Hom.: 0 Cov.: 31 AF XY: 0.000189 AC XY: 14AN XY: 74252
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 03, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 14, 2018 | - - |
Computational scores
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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