rs55832242

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117
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]

Genome browser will be placed here

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
SPTA1NM_003126.4 linkc.*111_*132delTGTGTGTGTGTGTGTGTGTGTG 3_prime_UTR_variant Exon 52 of 52 ENST00000643759.2 NP_003117.2 P02549-1
OR10Z1NM_001004478.2 linkc.*3765_*3786delACACACACACACACACACACAC 3_prime_UTR_variant Exon 2 of 2 ENST00000641002.1 NP_001004478.1 Q8NGY1A0A126GV63

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPTA1ENST00000643759 linkc.*111_*132delTGTGTGTGTGTGTGTGTGTGTG 3_prime_UTR_variant Exon 52 of 52 NM_003126.4 ENSP00000495214.1 P02549-1
OR10Z1ENST00000641002.1 linkc.*3765_*3786delACACACACACACACACACACAC 3_prime_UTR_variant Exon 2 of 2 NM_001004478.2 ENSP00000493003.1 Q8NGY1

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
Gnomad4 AFR exome
AF:
0.0000666
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000917
Gnomad4 OTH exome
AF:
0.00
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
Gnomad4 AFR
AF:
0.0000260
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs55832242; hg19: chr1-158580921; API