rs10459853

Variant names:

• chr16-84383036-C-G
• rs10459853
• NM_014861.4:c.99+14322C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-84383036-C-G
• chr16-84383036-C-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.99+14322C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,196 control chromosomes in the GnomAD database, including 1,676 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 (1676 hom., cov: 32)
• Consequence: ATP2C2 NM_014861.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 4 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]

ENSG00000301479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP2C2	NM_014861.4	c.99+14322C>G		intron_variant	Intron 1 of 26	ENST00000262429.9	NP_055676.3
ATP2C2	NM_001286527.3	c.99+14322C>G		intron_variant	Intron 1 of 27		NP_001273456.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP2C2	ENST00000262429.9	c.99+14322C>G		intron_variant	Intron 1 of 26	1	NM_014861.4	ENSP00000262429.4
ATP2C2	ENST00000416219.7	c.99+14322C>G		intron_variant	Intron 1 of 27	1		ENSP00000397925.2
ENSG00000301479	ENST00000779109.1	n.486+268G>C		intron_variant	Intron 2 of 2
ENSG00000301479	ENST00000779110.1	n.240-1462G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21597 AN: 152078 Hom.: 1680 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.142 AC: 21599 AN: 152196 Hom.: 1676 Cov.: 32 AF XY: 0.142 AC XY: 10567 AN XY: 74404

African (AFR) AF: 0.131 AC: 5437 AN: 41536

American (AMR) AF: 0.158 AC: 2419 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 394 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1495 AN: 5168

South Asian (SAS) AF: 0.139 AC: 668 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1319 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9515 AN: 67996

Other (OTH) AF: 0.121 AC: 255 AN: 2106

Alfa AF: 0.0774 Hom.: 91

Bravo AF: 0.146

Asia WGS AF: 0.203 AC: 703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.48
PhyloP100		0.52
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: rs10459853; hg19: chr16-84416642;