16-28878165-C-A

Position:

• chr16-28878165-C-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000691192.2(ATP2A1-AS1):​n.1772G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 150,134 control chromosomes in the GnomAD database, including 9,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (9471 hom., cov: 28)
• Consequence: ATP2A1-AS1 ENST00000691192.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.48

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 16-28878165-C-A is Benign according to our data. Variant chr16-28878165-C-A is described in ClinVar as [Benign]. Clinvar id is 671198.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP2A1-AS1	ENST00000691192.2	n.1772G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 51466 AN: 150016 Hom.: 9442 Cov.: 28

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.343 AC: 51560 AN: 150134 Hom.: 9471 Cov.: 28 AF XY: 0.342 AC XY: 25026 AN XY: 73188

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.311

Alfa AF: 0.356 Hom.: 8452

Bravo AF: 0.339

Asia WGS AF: 0.274 AC: 951 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 16, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3888190; hg19: chr16-28889486;