rs10132778
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001355436.2(SPTB):āc.4121A>Gā(p.His1374Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 1,614,044 control chromosomes in the GnomAD database, including 1,041 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001355436.2 missense
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.4121A>G | p.His1374Arg | missense_variant | 20/36 | ENST00000644917.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTB | ENST00000644917.1 | c.4121A>G | p.His1374Arg | missense_variant | 20/36 | NM_001355436.2 | P1 | ||
SPTB | ENST00000553938.5 | c.116A>G | p.His39Arg | missense_variant | 1/18 | 1 | |||
SPTB | ENST00000389722.7 | c.4121A>G | p.His1374Arg | missense_variant | 19/35 | 2 | P1 | ||
SPTB | ENST00000389720.4 | c.4121A>G | p.His1374Arg | missense_variant | 20/32 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0347 AC: 5272AN: 152092Hom.: 98 Cov.: 32
GnomAD3 exomes AF: 0.0328 AC: 8254AN: 251390Hom.: 189 AF XY: 0.0348 AC XY: 4724AN XY: 135876
GnomAD4 exome AF: 0.0326 AC: 47651AN: 1461834Hom.: 944 Cov.: 33 AF XY: 0.0339 AC XY: 24677AN XY: 727220
GnomAD4 genome ? AF: 0.0346 AC: 5271AN: 152210Hom.: 97 Cov.: 32 AF XY: 0.0344 AC XY: 2559AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 22, 2023 | - - |
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