chr19-50423748-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003121.5(SPIB):c.483C>T(p.Ser161=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,607,342 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 6 hom. )
Consequence
SPIB
NM_003121.5 synonymous
NM_003121.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.07
Genes affected
SPIB (HGNC:11242): (Spi-B transcription factor) The protein encoded by this gene is a transcriptional activator that binds to the PU-box (5'-GAGGAA-3') and acts as a lymphoid-specific enhancer. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 19-50423748-C-T is Benign according to our data. Variant chr19-50423748-C-T is described in ClinVar as [Benign]. Clinvar id is 784719.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-6.07 with no splicing effect.
BS2
?
High AC in GnomAd at 217 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPIB | NM_003121.5 | c.483C>T | p.Ser161= | synonymous_variant | 5/6 | ENST00000595883.6 | |
SPIB | NM_001244000.2 | c.390C>T | p.Ser130= | synonymous_variant | 5/6 | ||
SPIB | NM_001243999.2 | c.483C>T | p.Ser161= | synonymous_variant | 5/6 | ||
SPIB | NM_001243998.2 | c.210C>T | p.Ser70= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPIB | ENST00000595883.6 | c.483C>T | p.Ser161= | synonymous_variant | 5/6 | 1 | NM_003121.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00143 AC: 217AN: 152110Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00116 AC: 269AN: 232424Hom.: 0 AF XY: 0.00115 AC XY: 145AN XY: 126356
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GnomAD4 exome AF: 0.00218 AC: 3177AN: 1455114Hom.: 6 Cov.: 32 AF XY: 0.00208 AC XY: 1508AN XY: 723314
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GnomAD4 genome ? AF: 0.00143 AC: 217AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74448
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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 | Jul 11, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at