1-158611166-C-CACACAT
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BS2_Supporting
The NM_003126.4(SPTA1):c.*97_*98insATGTGT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000389 in 1,387,628 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.0021 ( 2 hom., cov: 28)
Exomes 𝑓: 0.00019 ( 2 hom. )
Consequence
SPTA1
NM_003126.4 3_prime_UTR
NM_003126.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.26
Genes affected
OR10Z1 (HGNC:14996): (olfactory receptor family 10 subfamily Z member 1) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]
SPTA1 (HGNC:11272): (spectrin alpha, erythrocytic 1) This gene encodes a member of a family of molecular scaffold proteins that link the plasma membrane to the actin cytoskeleton and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. The encoded protein is primarily composed of 22 spectrin repeats which are involved in dimer formation. It forms a component of the erythrocyte plasma membrane. Mutations in this gene result in a variety of hereditary red blood cell disorders, including elliptocytosis-2, pyropoikilocytosis, and spherocytosis, type 3. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 AD,AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR10Z1 | NM_001004478.2 | c.*3786_*3787insACACAT | 3_prime_UTR_variant | 2/2 | ENST00000641002.1 | ||
SPTA1 | NM_003126.4 | c.*97_*98insATGTGT | 3_prime_UTR_variant | 52/52 | ENST00000643759.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR10Z1 | ENST00000641002.1 | c.*3786_*3787insACACAT | 3_prime_UTR_variant | 2/2 | NM_001004478.2 | P1 | |||
SPTA1 | ENST00000643759.2 | c.*97_*98insATGTGT | 3_prime_UTR_variant | 52/52 | NM_003126.4 | P1 | |||
SPTA1 | ENST00000485680.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00208 AC: 307AN: 147330Hom.: 2 Cov.: 28
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GnomAD4 exome AF: 0.000185 AC: 230AN: 1240194Hom.: 2 Cov.: 17 AF XY: 0.000153 AC XY: 96AN XY: 625760
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GnomAD4 genome AF: 0.00210 AC: 310AN: 147434Hom.: 2 Cov.: 28 AF XY: 0.00187 AC XY: 134AN XY: 71714
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Elliptocytosis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Pyropoikilocytosis, hereditary Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Spherocytosis, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at