1-158611131-GCACACACACACACACACACACA-GCACACACACACACA

Variant names:

• chr1-158611131-GCACACACA-G
• rs55832242
• NM_003126.4:c.*125_*132delTGTGTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_003126.4(SPTA1):​c.*125_*132delTGTGTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000721 in 671,102 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00088 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00068 (1 hom.)
• Consequence: SPTA1 NM_003126.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPTA1	NM_003126.4	c.*125_*132delTGTGTGTG		3_prime_UTR_variant	Exon 52 of 52	ENST00000643759.2	NP_003117.2
OR10Z1	NM_001004478.2	c.*3779_*3786delACACACAC		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.*125_*132delTGTGTGTG		3_prime_UTR_variant	Exon 52 of 52		NM_003126.4	ENSP00000495214.1
OR10Z1	ENST00000641002.1	c.*3779_*3786delACACACAC		3_prime_UTR_variant	Exon 2 of 2		NM_001004478.2	ENSP00000493003.1

Frequencies

GnomAD3 genomes AF: 0.000869 AC: 125 AN: 143812 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000559

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000618

Gnomad SAS AF: 0.000226

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000454

Gnomad OTH AF: 0.000512

GnomAD4 exome AF: 0.000677 AC: 357 AN: 527180 Hom.: 1 AF XY: 0.000675 AC XY: 189 AN XY: 279798

Gnomad4 AFR exome AF: 0.00447

Gnomad4 AMR exome AF: 0.000611

Gnomad4 ASJ exome AF: 0.000131

Gnomad4 EAS exome AF: 0.00154

Gnomad4 SAS exome AF: 0.000399

Gnomad4 FIN exome AF: 0.000197

Gnomad4 NFE exome AF: 0.000535

Gnomad4 OTH exome AF: 0.000977

GnomAD4 genome AF: 0.000882 AC: 127 AN: 143922 Hom.: 0 Cov.: 0 AF XY: 0.000776 AC XY: 54 AN XY: 69578

Gnomad4 AFR AF: 0.00288

Gnomad4 AMR AF: 0.000559

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000619

Gnomad4 SAS AF: 0.000226

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000454

Gnomad4 OTH AF: 0.000507

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;