1-158610763-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003126.4(SPTA1):​c.*500del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 152,718 control chromosomes in the GnomAD database, including 219 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.047 ( 218 hom., cov: 31)
Exomes 𝑓: 0.062 ( 1 hom. )

Consequence

SPTA1
NM_003126.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:3

Conservation

PhyloP100: 0.0510
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 1-158610763-TA-T is Benign according to our data. Variant chr1-158610763-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 292917.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR10Z1NM_001004478.2 linkuse as main transcriptc.*3390del 3_prime_UTR_variant 2/2 ENST00000641002.1
SPTA1NM_003126.4 linkuse as main transcriptc.*500del 3_prime_UTR_variant 52/52 ENST00000643759.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR10Z1ENST00000641002.1 linkuse as main transcriptc.*3390del 3_prime_UTR_variant 2/2 NM_001004478.2 P1
SPTA1ENST00000643759.2 linkuse as main transcriptc.*500del 3_prime_UTR_variant 52/52 NM_003126.4 P1P02549-1

Frequencies

GnomAD3 genomes
AF:
0.0470
AC:
7143
AN:
152052
Hom.:
218
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0115
Gnomad AMI
AF:
0.0680
Gnomad AMR
AF:
0.0415
Gnomad ASJ
AF:
0.0381
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.0199
Gnomad FIN
AF:
0.0988
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0675
Gnomad OTH
AF:
0.0469
GnomAD4 exome
AF:
0.0620
AC:
34
AN:
548
Hom.:
1
Cov.:
0
AF XY:
0.0852
AC XY:
23
AN XY:
270
show subpopulations
Gnomad4 AMR exome
AF:
0.0263
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0333
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0752
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0469
AC:
7144
AN:
152170
Hom.:
218
Cov.:
31
AF XY:
0.0478
AC XY:
3557
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0115
Gnomad4 AMR
AF:
0.0415
Gnomad4 ASJ
AF:
0.0381
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.0201
Gnomad4 FIN
AF:
0.0988
Gnomad4 NFE
AF:
0.0675
Gnomad4 OTH
AF:
0.0464
Alfa
AF:
0.0548
Hom.:
36
Bravo
AF:
0.0412
Asia WGS
AF:
0.00754
AC:
26
AN:
3462

ClinVar

Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Elliptocytosis Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Pyropoikilocytosis, hereditary Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Spherocytosis, Recessive Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs34122435; hg19: chr1-158580553; API