rs8048576

Variant names:

• chr16-84389428-G-A
• rs8048576
• NM_014861.4:c.100-9071G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-84389428-G-A
• chr16-84389428-G-C
• chr16-84389428-G-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.100-9071G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,228 control chromosomes in the GnomAD database, including 2,506 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 0.17 (2506 hom., cov: 34)
• Consequence: ATP2C2 NM_014861.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 12 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 = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP2C2	NM_014861.4	c.100-9071G>A		intron_variant	Intron 1 of 26	ENST00000262429.9	NP_055676.3
ATP2C2	NM_001286527.3	c.100-9071G>A		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.100-9071G>A		intron_variant	Intron 1 of 26	1	NM_014861.4	ENSP00000262429.4
ATP2C2	ENST00000416219.7	c.100-9071G>A		intron_variant	Intron 1 of 27	1		ENSP00000397925.2
ENSG00000301479	ENST00000779109.1	n.242+899C>T		intron_variant	Intron 1 of 2
ENSG00000301479	ENST00000779110.1	n.239+899C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25674 AN: 152110 Hom.: 2489 Cov.: 34

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.169 AC: 25741 AN: 152228 Hom.: 2506 Cov.: 34 AF XY: 0.171 AC XY: 12749 AN XY: 74422

African (AFR) AF: 0.207 AC: 8598 AN: 41508

American (AMR) AF: 0.241 AC: 3681 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1880 AN: 5174

South Asian (SAS) AF: 0.129 AC: 624 AN: 4830

European-Finnish (FIN) AF: 0.156 AC: 1651 AN: 10610

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8040 AN: 68034

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.139 Hom.: 5569

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		-2.5
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: rs8048576; hg19: chr16-84423034;