rs7350833

chr16-84380558-G-Cchr16-84380558-G-T

Variant summary

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

The NM_014861.4(ATP2C2):c.99+11844G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,098 control chromosomes in the GnomAD database, including 5,509 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 0.26 (5509 hom., cov: 32)
• Consequence: ATP2C2 NM_014861.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

ATP2C2 (HGNC:29103): (ATPase secretory pathway Ca2+ transporting 2) Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; cellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP2C2	NM_014861.4	c.99+11844G>C		intron_variant		ENST00000262429.9
ATP2C2	NM_001286527.3	c.99+11844G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP2C2	ENST00000262429.9	c.99+11844G>C		intron_variant		1	NM_014861.4	P1
ATP2C2	ENST00000416219.6	c.99+11844G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39913 AN: 151980 Hom.: 5507 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.263 AC: 39936 AN: 152098 Hom.: 5509 Cov.: 32 AF XY: 0.261 AC XY: 19387 AN XY: 74330

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.273

Alfa AF: 0.176 Hom.: 412

Bravo AF: 0.259

Asia WGS AF: 0.233 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.0
Dann	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7350833; hg19: chr16-84414164;