1-158611131-GCACACACACACACACACACACA-GCACACACACACACACACACACACACA

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTA1	NM_003126.4	c.*129_*132dupTGTG		3_prime_UTR_variant	Exon 52 of 52	ENST00000643759.2	NP_003117.2
OR10Z1	NM_001004478.2	c.*3783_*3786dupACAC		3_prime_UTR_variant	Exon 2 of 2	ENST00000641002.1	NP_001004478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPTA1	ENST00000643759	c.*129_*132dupTGTG		3_prime_UTR_variant	Exon 52 of 52		NM_003126.4	ENSP00000495214.1
OR10Z1	ENST00000641002.1	c.*3783_*3786dupACAC		3_prime_UTR_variant	Exon 2 of 2		NM_001004478.2	ENSP00000493003.1

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

Gnomad4 AFR exome AF: 0.0736

Gnomad4 AMR exome AF: 0.0443

Gnomad4 ASJ exome AF: 0.0556

Gnomad4 EAS exome AF: 0.0369

Gnomad4 SAS exome AF: 0.0344

Gnomad4 FIN exome AF: 0.0528

Gnomad4 NFE exome AF: 0.0788

Gnomad4 OTH exome AF: 0.0671

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

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0610

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0550

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0847

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55832242; hg19: chr1-158580921;