16-84449625-G-A

Variant names:

• chr16-84449625-G-A
• rs247889
• NM_014861.4:c.1660+936G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014861.4(ATP2C2):​c.1660+936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,080 control chromosomes in the GnomAD database, including 4,330 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 0.21 (4330 hom., cov: 32)
• Consequence: ATP2C2 NM_014861.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

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]

ENSG00000305404 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014861.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP2C2	NM_014861.4	MANE Select	c.1660+936G>A		intron	N/A	NP_055676.3
	ATP2C2	NM_001286527.3		c.1660+936G>A		intron	N/A	NP_001273456.2
	ATP2C2	NM_001291454.2		c.1207+936G>A		intron	N/A	NP_001278383.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP2C2	ENST00000262429.9	TSL:1 MANE Select	c.1660+936G>A		intron	N/A	ENSP00000262429.4
	ATP2C2	ENST00000416219.7	TSL:1	c.1660+936G>A		intron	N/A	ENSP00000397925.2
	ATP2C2	ENST00000420010.6	TSL:2	n.1333+936G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31819 AN: 151962 Hom.: 4335 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.209 AC: 31799 AN: 152080 Hom.: 4330 Cov.: 32 AF XY: 0.215 AC XY: 15945 AN XY: 74330

African (AFR) AF: 0.0566 AC: 2351 AN: 41508

American (AMR) AF: 0.191 AC: 2919 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3472

East Asian (EAS) AF: 0.0459 AC: 238 AN: 5184

South Asian (SAS) AF: 0.219 AC: 1052 AN: 4806

European-Finnish (FIN) AF: 0.413 AC: 4352 AN: 10550

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19244 AN: 67968

Other (OTH) AF: 0.198 AC: 417 AN: 2110

Alfa AF: 0.230 Hom.: 602

Bravo AF: 0.186

Asia WGS AF: 0.115 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.86
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs247889; hg19: chr16-84483231;