GeneBe

rs55832242

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

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. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Publications

1 publications found
Variant links:
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003126.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SPTA1
NM_003126.4
MANE Select
c.*111_*132delTGTGTGTGTGTGTGTGTGTGTG
3_prime_UTR
Exon 52 of 52NP_003117.2P02549-1
OR10Z1
NM_001004478.2
MANE Select
c.*3765_*3786delACACACACACACACACACACAC
3_prime_UTR
Exon 2 of 2NP_001004478.1A0A126GV63

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SPTA1
ENST00000643759.2
MANE Select
c.*111_*132delTGTGTGTGTGTGTGTGTGTGTG
3_prime_UTR
Exon 52 of 52ENSP00000495214.1P02549-1
OR10Z1
ENST00000641002.1
MANE Select
c.*3765_*3786delACACACACACACACACACACAC
3_prime_UTR
Exon 2 of 2ENSP00000493003.1Q8NGY1
SPTA1
ENST00000485680.1
TSL:3
n.*55_*76delTGTGTGTGTGTGTGTGTGTGTG
downstream_gene
N/A

Frequencies

GnomAD3 genomes
AF:
0.00000695
AC:
1
AN:
143812
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000260
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000758
AC:
4
AN:
527506
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
279978
show subpopulations
African (AFR)
AF:
0.0000666
AC:
1
AN:
15004
American (AMR)
AF:
0.00
AC:
0
AN:
29460
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15222
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26088
South Asian (SAS)
AF:
0.00
AC:
0
AN:
55162
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
30506
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2320
European-Non Finnish (NFE)
AF:
0.00000917
AC:
3
AN:
327102
Other (OTH)
AF:
0.00
AC:
0
AN:
26642
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.413
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.00000695
AC:
1
AN:
143812
Hom.:
0
Cov.:
0
AF XY:
0.0000144
AC XY:
1
AN XY:
69452
show subpopulations
African (AFR)
AF:
0.0000260
AC:
1
AN:
38396
American (AMR)
AF:
0.00
AC:
0
AN:
14302
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3378
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4854
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4432
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9196
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
302
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
66104
Other (OTH)
AF:
0.00
AC:
0
AN:
1952
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.775
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs55832242; hg19: chr1-158580921; API