rs7142689
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001355436.2(SPTB):c.5799-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,613,866 control chromosomes in the GnomAD database, including 12,813 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001355436.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTB | NM_001355436.2 | c.5799-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTB | ENST00000644917.1 | c.5799-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001355436.2 | P1 | ||||
SPTB | ENST00000553938.5 | c.1794-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
SPTB | ENST00000389720.4 | c.5799-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
SPTB | ENST00000389722.7 | c.5799-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.161 AC: 24551AN: 152042Hom.: 2835 Cov.: 33
GnomAD3 exomes AF: 0.0992 AC: 24938AN: 251318Hom.: 1917 AF XY: 0.0938 AC XY: 12738AN XY: 135864
GnomAD4 exome AF: 0.107 AC: 155960AN: 1461704Hom.: 9961 Cov.: 33 AF XY: 0.104 AC XY: 75760AN XY: 727174
GnomAD4 genome AF: 0.162 AC: 24602AN: 152162Hom.: 2852 Cov.: 33 AF XY: 0.157 AC XY: 11706AN XY: 74392
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 27, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Elliptocytosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spherocytosis, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at