rs28525570

Variant names:

• chr1-158618068-G-A
• rs28525570
• NM_003126.4:c.6531-12C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-158618068-G-A
• chr1-158618068-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_003126.4(SPTA1):​c.6531-12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,602,240 control chromosomes in the GnomAD database, including 60,252 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.25 (5121 hom., cov: 32)
  • Exomes 𝑓: 0.27 (55131 hom.)
• Consequence: SPTA1 NM_003126.4 intron
• Scores: Splicing: ADA: 0.0004991
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:1 B:6
• Conservation: PhyloP100: 0.574

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 1-158618068-G-A is Benign according to our data. Variant chr1-158618068-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 258954.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Likely_pathogenic=1, Benign=3, Uncertain_significance=1}.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTA1	NM_003126.4	c.6531-12C>T		intron_variant	Intron 45 of 51	ENST00000643759.2	NP_003117.2
SPTA1	XM_011509916.3	c.6531-12C>T		intron_variant	Intron 46 of 52		XP_011508218.1
SPTA1	XM_011509917.4	c.6531-480C>T		intron_variant	Intron 45 of 50		XP_011508219.1
SPTA1	XM_047428883.1	c.6210-12C>T		intron_variant	Intron 45 of 51		XP_047284839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTA1	ENST00000643759.2	c.6531-12C>T		intron_variant	Intron 45 of 51		NM_003126.4	ENSP00000495214.1
SPTA1	ENST00000492934.1	n.34C>T		non_coding_transcript_exon_variant	Exon 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38595 AN: 151962 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.261

GnomAD3 exomes AF: 0.254 AC: 63402 AN: 249186 Hom.: 8413 AF XY: 0.259 AC XY: 35021 AN XY: 135198

Gnomad AFR exome AF: 0.198

Gnomad AMR exome AF: 0.171

Gnomad ASJ exome AF: 0.349

Gnomad EAS exome AF: 0.185

Gnomad SAS exome AF: 0.250

Gnomad FIN exome AF: 0.292

Gnomad NFE exome AF: 0.284

Gnomad OTH exome AF: 0.259

GnomAD4 exome AF: 0.271 AC: 393274 AN: 1450160 Hom.: 55131 Cov.: 32 AF XY: 0.272 AC XY: 196331 AN XY: 721926

Gnomad4 AFR exome AF: 0.197

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.203

Gnomad4 SAS exome AF: 0.245

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.280

Gnomad4 OTH exome AF: 0.263

GnomAD4 genome AF: 0.254 AC: 38604 AN: 152080 Hom.: 5121 Cov.: 32 AF XY: 0.255 AC XY: 18981 AN XY: 74334

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.264

Alfa AF: 0.214 Hom.: 769

Bravo AF: 0.242

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:1 Benign:6

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Benign:2

Nov 30, 2021

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SPTA1: BS1, BS2 -

May 24, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Commonly referred to as the AlphaLELY allele, this variant is a low expression allele that results in partial skipping of exon 46 and expression of hereditary elliptocytosis when in trans with a pathogenic SPTA1 variant (Wilmotte et al., 1999); This variant has been reported multiple times in association with hereditary elliptocytosis when present in trans with a pathogenic SPTA1 variant (Russo et al., 2018; Aggarwal et al., 2020; Suzuki et al., 2021) This variant is associated with the following publications: (PMID: 10192450, 29396846, 31602632, 32287101, 29484404, 30298500, 32581362) -

not specified Uncertain:1 Benign:1

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hemolytic anemia Pathogenic:1

-

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Elliptocytosis 2 Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Hereditary spherocytosis type 3 Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Pyropoikilocytosis, hereditary Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00050
dbscSNV1_RF	Benign	0.26
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs28525570; hg19: chr1-158587858; COSMIC: COSV63760163; COSMIC: COSV63760163;