NM_003126.4:c.*129_*132dupTGTG

Variant names:

• chr1-158611131-G-GCACA
• rs55832242
• NM_003126.4:c.*129_*132dupTGTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003126.4(SPTA1):​c.*129_*132dupTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.089 (584 hom., cov: 0)
  • Exomes 𝑓: 0.067 (230 hom.)
• Consequence: SPTA1 NM_003126.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPTA1	NM_003126.4	MANE Select	c.*129_*132dupTGTG		3_prime_UTR	Exon 52 of 52	NP_003117.2	P02549-1
	OR10Z1	NM_001004478.2	MANE Select	c.*3783_*3786dupACAC		3_prime_UTR	Exon 2 of 2	NP_001004478.1	A0A126GV63

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPTA1	ENST00000643759.2	MANE Select	c.*129_*132dupTGTG		3_prime_UTR	Exon 52 of 52	ENSP00000495214.1	P02549-1
	OR10Z1	ENST00000641002.1	MANE Select	c.*3783_*3786dupACAC		3_prime_UTR	Exon 2 of 2	ENSP00000493003.1	Q8NGY1
	SPTA1	ENST00000485680.1	TSL:3	n.*73_*76dupTGTG		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0889 AC: 12769 AN: 143686 Hom.: 583 Cov.: 0

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0610

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0200

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0835

GnomAD4 exome AF: 0.0671 AC: 35121 AN: 523798 Hom.: 230 Cov.: 0 AF XY: 0.0653 AC XY: 18151 AN XY: 277932

African (AFR) AF: 0.0736 AC: 1096 AN: 14894

American (AMR) AF: 0.0443 AC: 1297 AN: 29304

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 842 AN: 15154

East Asian (EAS) AF: 0.0369 AC: 956 AN: 25936

South Asian (SAS) AF: 0.0344 AC: 1889 AN: 54860

European-Finnish (FIN) AF: 0.0528 AC: 1601 AN: 30314

Middle Eastern (MID) AF: 0.0419 AC: 97 AN: 2316

European-Non Finnish (NFE) AF: 0.0788 AC: 25572 AN: 324608

Other (OTH) AF: 0.0671 AC: 1771 AN: 26412

GnomAD4 genome AF: 0.0888 AC: 12775 AN: 143796 Hom.: 584 Cov.: 0 AF XY: 0.0846 AC XY: 5882 AN XY: 69508

African (AFR) AF: 0.0922 AC: 3548 AN: 38476

American (AMR) AF: 0.0619 AC: 886 AN: 14316

Ashkenazi Jewish (ASJ) AF: 0.0610 AC: 206 AN: 3376

East Asian (EAS) AF: 0.0378 AC: 183 AN: 4840

South Asian (SAS) AF: 0.0353 AC: 156 AN: 4424

European-Finnish (FIN) AF: 0.0550 AC: 505 AN: 9180

Middle Eastern (MID) AF: 0.0145 AC: 4 AN: 276

European-Non Finnish (NFE) AF: 0.106 AC: 6973 AN: 66040

Other (OTH) AF: 0.0847 AC: 167 AN: 1972

Alfa AF: 0.0663 Hom.: 292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs55832242; hg19: chr1-158580921;