16-28878386-CA-C

Position:

• chr16-28878386-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000691192.2(ATP2A1-AS1):​n.1550del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.34 (9453 hom., cov: 0)
  • Exomes 𝑓: 0.35 (20120 hom.)
• Consequence: ATP2A1-AS1 ENST00000691192.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

Genes affected

ATP2A1-AS1 (HGNC:51370): (ATP2A1 antisense RNA 1)

ATP2A1 (HGNC:811): (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1) This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen, and is involved in muscular excitation and contraction. Mutations in this gene cause some autosomal recessive forms of Brody disease, characterized by increasing impairment of muscular relaxation during exercise. Alternative splicing results in three transcript variants encoding different isoforms. [provided by RefSeq, Oct 2013]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 16-28878386-CA-C is Benign according to our data. Variant chr16-28878386-CA-C is described in ClinVar as [Benign]. Clinvar id is 1178419.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP2A1-AS1	ENST00000691192.2	n.1550del		non_coding_transcript_exon_variant	1/1
ATP2A1	ENST00000357084.7			upstream_gene_variant		2		ENSP00000349595	A1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51639 AN: 151678 Hom.: 9424 Cov.: 0

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.345 AC: 107406 AN: 311030 Hom.: 20120 Cov.: 0 AF XY: 0.336 AC XY: 55591 AN XY: 165486

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.455

Gnomad4 ASJ exome AF: 0.271

Gnomad4 EAS exome AF: 0.124

Gnomad4 SAS exome AF: 0.222

Gnomad4 FIN exome AF: 0.418

Gnomad4 NFE exome AF: 0.389

Gnomad4 OTH exome AF: 0.344

GnomAD4 genome AF: 0.341 AC: 51733 AN: 151796 Hom.: 9453 Cov.: 0 AF XY: 0.339 AC XY: 25138 AN XY: 74186

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.308

Alfa AF: 0.180 Hom.: 389

Bravo AF: 0.338

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

- -

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: rs140143522; hg19: chr16-28889707; COSMIC: COSV59463027;