chr19-16851427-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001297595.2(SIN3B):c.742C>T(p.Pro248Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000374 in 1,603,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001297595.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SIN3B | NM_001297595.2 | c.742C>T | p.Pro248Ser | missense_variant | 6/19 | ENST00000248054.10 | |
SIN3B | NM_015260.4 | c.742C>T | p.Pro248Ser | missense_variant | 6/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIN3B | ENST00000248054.10 | c.742C>T | p.Pro248Ser | missense_variant | 6/19 | 1 | NM_001297595.2 | P1 | |
SIN3B | ENST00000379803.5 | c.742C>T | p.Pro248Ser | missense_variant | 6/20 | 1 | |||
SIN3B | ENST00000596802.5 | c.742C>T | p.Pro248Ser | missense_variant | 6/8 | 1 | |||
SIN3B | ENST00000596638.1 | c.178C>T | p.Pro60Ser | missense_variant | 3/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000248 AC: 6AN: 241720Hom.: 0 AF XY: 0.00000763 AC XY: 1AN XY: 131092
GnomAD4 exome AF: 0.00000345 AC: 5AN: 1451254Hom.: 0 Cov.: 31 AF XY: 0.00000277 AC XY: 2AN XY: 721436
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.742C>T (p.P248S) alteration is located in exon 6 (coding exon 6) of the SIN3B gene. This alteration results from a C to T substitution at nucleotide position 742, causing the proline (P) at amino acid position 248 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at