chr19-50423712-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003121.5(SPIB):c.447T>C(p.Asp149=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,613,170 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 (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
SPIB
NM_003121.5 synonymous
NM_003121.5 synonymous
Scores
5
Clinical Significance
Conservation
PhyloP100: -0.726
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_addAF=-0.476931).
BP6
?
Variant 19-50423712-T-C is Benign according to our data. Variant chr19-50423712-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 753149.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.726 with no splicing effect.
BS2
?
High AC in GnomAd at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPIB | NM_003121.5 | c.447T>C | p.Asp149= | synonymous_variant | 5/6 | ENST00000595883.6 | |
SPIB | NM_001244000.2 | c.354T>C | p.Asp118= | synonymous_variant | 5/6 | ||
SPIB | NM_001243999.2 | c.447T>C | p.Asp149= | synonymous_variant | 5/6 | ||
SPIB | NM_001243998.2 | c.174T>C | p.Asp58= | synonymous_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPIB | ENST00000595883.6 | c.447T>C | p.Asp149= | synonymous_variant | 5/6 | 1 | NM_003121.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152094Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000162 AC: 40AN: 246800Hom.: 0 AF XY: 0.000149 AC XY: 20AN XY: 133920
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GnomAD4 exome AF: 0.000212 AC: 309AN: 1460958Hom.: 0 Cov.: 32 AF XY: 0.000230 AC XY: 167AN XY: 726706
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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 | Invitae | Aug 07, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
D;D
Vest4
GERP RS
Splicing
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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