rs55832242
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chr1-158611131-GCACACACACACACACACACACA-G
- chr1-158611131-GCACACACACACACACACACACA-GCA
- chr1-158611131-GCACACACACACACACACACACA-GCACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACACACACACA
- chr1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACACACACACACACACACACACA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003126.4(SPTA1):c.*111_*132delTGTGTGTGTGTGTGTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 671,318 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000070 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000076 ( 0 hom. )
Consequence
SPTA1
NM_003126.4 3_prime_UTR
NM_003126.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.117
Genes affected
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]
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SPTA1 | NM_003126.4 | c.*111_*132delTGTGTGTGTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 52 of 52 | ENST00000643759.2 | NP_003117.2 | ||
| OR10Z1 | NM_001004478.2 | c.*3765_*3786delACACACACACACACACACACAC | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000641002.1 | NP_001004478.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SPTA1 | ENST00000643759 | c.*111_*132delTGTGTGTGTGTGTGTGTGTGTG | 3_prime_UTR_variant | Exon 52 of 52 | NM_003126.4 | ENSP00000495214.1 | ||||
| OR10Z1 | ENST00000641002.1 | c.*3765_*3786delACACACACACACACACACACAC | 3_prime_UTR_variant | Exon 2 of 2 | NM_001004478.2 | ENSP00000493003.1 | ||||
| SPTA1 | ENST00000485680.1 | n.*55_*76delTGTGTGTGTGTGTGTGTGTGTG | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes 0.00000695 AC: 1AN: 143812Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000758 AC: 4AN: 527506Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 279978
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GnomAD4 genome 0.00000695 AC: 1AN: 143812Hom.: 0 Cov.: 0 AF XY: 0.0000144 AC XY: 1AN XY: 69452
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at