rs1741487
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001355436.2(SPTB):āc.4476T>Cā(p.Leu1492=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,602,920 control chromosomes in the GnomAD database, including 61,885 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001355436.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTB | NM_001355436.2 | c.4476T>C | p.Leu1492= | splice_region_variant, synonymous_variant | 22/36 | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTB | ENST00000644917.1 | c.4476T>C | p.Leu1492= | splice_region_variant, synonymous_variant | 22/36 | NM_001355436.2 | P1 | ||
SPTB | ENST00000553938.5 | c.471T>C | p.Leu157= | splice_region_variant, synonymous_variant | 3/18 | 1 | |||
SPTB | ENST00000389722.7 | c.4476T>C | p.Leu1492= | splice_region_variant, synonymous_variant | 21/35 | 2 | P1 | ||
SPTB | ENST00000389720.4 | c.4476T>C | p.Leu1492= | splice_region_variant, synonymous_variant | 22/32 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.341 AC: 51806AN: 151738Hom.: 11166 Cov.: 32
GnomAD3 exomes AF: 0.267 AC: 66169AN: 248078Hom.: 10463 AF XY: 0.269 AC XY: 36060AN XY: 134136
GnomAD4 exome AF: 0.251 AC: 363768AN: 1451064Hom.: 50692 Cov.: 32 AF XY: 0.254 AC XY: 183048AN XY: 722028
GnomAD4 genome ? AF: 0.342 AC: 51871AN: 151856Hom.: 11193 Cov.: 32 AF XY: 0.340 AC XY: 25207AN XY: 74226
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
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 | - - |
Hereditary spherocytosis type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at