rs429313

chr16-84464239-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146503.1(ATP2C2-AS1):n.59-1240G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 153,134 control chromosomes in the GnomAD database, including 2,449 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.16 (2428 hom., cov: 32)
  • Exomes 𝑓: 0.20 (21 hom.)
• Consequence: ATP2C2-AS1 NR_146503.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

ATP2C2-AS1 (HGNC:53167): (ATP2C2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP2C2-AS1	NR_146503.1	n.59-1240G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP2C2-AS1	ENST00000565700.1	n.59-1240G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24179 AN: 151864 Hom.: 2429 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0849

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.198 AC: 228 AN: 1150 Hom.: 21 AF XY: 0.208 AC XY: 125 AN XY: 600

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.200

Gnomad4 ASJ exome AF: 0.167

Gnomad4 EAS exome AF: 0.143

Gnomad4 SAS exome AF: 0.185

Gnomad4 FIN exome AF: 0.286

Gnomad4 NFE exome AF: 0.196

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.159 AC: 24183 AN: 151984 Hom.: 2428 Cov.: 32 AF XY: 0.164 AC XY: 12186 AN XY: 74304

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0855

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.152

Alfa AF: 0.191 Hom.: 4890

Bravo AF: 0.147

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.62
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429313; hg19: chr16-84497845;