NM_014861.4:c.1504-505C>T

Variant names:

• chr16-84448028-C-T
• rs8062058
• NM_014861.4:c.1504-505C>T

Variant summary

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

The NM_014861.4(ATP2C2):​c.1504-505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,908 control chromosomes in the GnomAD database, including 1,552 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 0.14 (1552 hom., cov: 31)
• Consequence: ATP2C2 NM_014861.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP2C2	NM_014861.4	c.1504-505C>T		intron_variant	Intron 16 of 26	ENST00000262429.9	NP_055676.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2C2	ENST00000262429.9	c.1504-505C>T		intron_variant	Intron 16 of 26	1	NM_014861.4	ENSP00000262429.4

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20919 AN: 151792 Hom.: 1552 Cov.: 31

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.138 AC: 20926 AN: 151908 Hom.: 1552 Cov.: 31 AF XY: 0.136 AC XY: 10125 AN XY: 74234

African (AFR) AF: 0.170 AC: 7052 AN: 41378

American (AMR) AF: 0.104 AC: 1587 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.0317 AC: 153 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1579 AN: 10538

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9673 AN: 67954

Other (OTH) AF: 0.134 AC: 283 AN: 2110

Alfa AF: 0.134 Hom.: 222

Bravo AF: 0.137

Asia WGS AF: 0.0270 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.14
DANN	Benign	0.41
PhyloP100		-0.65
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: rs8062058; hg19: chr16-84481634;