rs148504156
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001355436.2(SPTB):c.4143C>T(p.Ser1381=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,614,148 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 0.000098 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
SPTB
NM_001355436.2 synonymous
NM_001355436.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.22
Genes affected
SPTB (HGNC:11274): (spectrin beta, erythrocytic) This locus encodes a member of the spectrin gene family. Spectrin proteins, along with ankyrin, play a role in cell membrane organization and stability. The protein encoded by this locus functions in stability of erythrocyte membranes, and mutations in this gene have been associated with spherocytosis type 2, hereditary elliptocytosis, and neonatal hemolytic anemia. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 14-64782413-G-A is Benign according to our data. Variant chr14-64782413-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 257113.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-4.22 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTB | NM_001355436.2 | c.4143C>T | p.Ser1381= | synonymous_variant | 20/36 | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTB | ENST00000644917.1 | c.4143C>T | p.Ser1381= | synonymous_variant | 20/36 | NM_001355436.2 | P1 | ||
SPTB | ENST00000553938.5 | c.138C>T | p.Ser46= | synonymous_variant | 1/18 | 1 | |||
SPTB | ENST00000389722.7 | c.4143C>T | p.Ser1381= | synonymous_variant | 19/35 | 2 | P1 | ||
SPTB | ENST00000389720.4 | c.4143C>T | p.Ser1381= | synonymous_variant | 20/32 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152198Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000278 AC: 70AN: 251424Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135900
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GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461832Hom.: 0 Cov.: 33 AF XY: 0.0000756 AC XY: 55AN XY: 727222
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GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74478
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ClinVar
Significance: Benign/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 | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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