rs1695769
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001355436.2(SPTB):c.*859C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,244 control chromosomes in the GnomAD database, including 1,749 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1749 hom., cov: 32)
Exomes 𝑓: 0.14 ( 0 hom. )
Consequence
SPTB
NM_001355436.2 3_prime_UTR
NM_001355436.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.85
Genes affected
PLEKHG3 (HGNC:20364): (pleckstrin homology and RhoGEF domain containing G3) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of small GTPase mediated signal transduction. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHG3 | NM_001308147.2 | c.*4744G>A | 3_prime_UTR_variant | 17/17 | ENST00000247226.13 | ||
SPTB | NM_001355436.2 | c.*859C>T | 3_prime_UTR_variant | 36/36 | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHG3 | ENST00000247226.13 | c.*4744G>A | 3_prime_UTR_variant | 17/17 | 1 | NM_001308147.2 | A2 | ||
SPTB | ENST00000644917.1 | c.*859C>T | 3_prime_UTR_variant | 36/36 | NM_001355436.2 | P1 | |||
PLEKHG3 | ENST00000634379.2 | c.*4744G>A | 3_prime_UTR_variant | 17/17 | 1 | P4 | |||
SPTB | ENST00000389722.7 | c.*859C>T | 3_prime_UTR_variant | 35/35 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.140 AC: 21329AN: 152052Hom.: 1751 Cov.: 32
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GnomAD4 exome AF: 0.135 AC: 10AN: 74Hom.: 0 Cov.: 0 AF XY: 0.188 AC XY: 9AN XY: 48
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GnomAD4 genome ? AF: 0.140 AC: 21346AN: 152170Hom.: 1749 Cov.: 32 AF XY: 0.138 AC XY: 10292AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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