rs1541254

Variant names:

• chr1-203683012-C-G
• rs1541254
• NM_001684.5:c.-194C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-203683012-C-G
• chr1-203683012-C-T

Variant summary

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

The NM_001684.5(ATP2B4):​c.-194C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 526,938 control chromosomes in the GnomAD database, including 200,205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.83 (53348 hom., cov: 31)
  • Exomes 𝑓: 0.88 (146857 hom.)
• Consequence: ATP2B4 NM_001684.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 12 publications found

Genes affected

ATP2B4 (HGNC:817): (ATPase plasma membrane Ca2+ transporting 4) The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells against very large concentration gradients and play a critical role in intracellular calcium homeostasis. The mammalian plasma membrane calcium ATPase isoforms are encoded by at least four separate genes and the diversity of these enzymes is further increased by alternative splicing of transcripts. The expression of different isoforms and splice variants is regulated in a developmental, tissue- and cell type-specific manner, suggesting that these pumps are functionally adapted to the physiological needs of particular cells and tissues. This gene encodes the plasma membrane calcium ATPase isoform 4. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001684.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP2B4	NM_001684.5	MANE Select	c.-194C>G		5_prime_UTR	Exon 2 of 21	NP_001675.3
	ATP2B4	NM_001001396.3		c.-194C>G		5_prime_UTR	Exon 2 of 22	NP_001001396.1
	ATP2B4	NM_001365783.2		c.-194C>G		5_prime_UTR	Exon 2 of 21	NP_001352712.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP2B4	ENST00000357681.10	TSL:1 MANE Select	c.-194C>G		5_prime_UTR	Exon 2 of 21	ENSP00000350310.5
	ATP2B4	ENST00000341360.7	TSL:1	c.-194C>G		5_prime_UTR	Exon 2 of 22	ENSP00000340930.2
	ATP2B4	ENST00000890814.1		c.-194C>G		5_prime_UTR	Exon 2 of 21	ENSP00000560873.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126207 AN: 151594 Hom.: 53340 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.859

GnomAD4 exome AF: 0.883 AC: 331173 AN: 375226 Hom.: 146857 Cov.: 5 AF XY: 0.883 AC XY: 171907 AN XY: 194740

African (AFR) AF: 0.669 AC: 7260 AN: 10854

American (AMR) AF: 0.921 AC: 12814 AN: 13912

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 10168 AN: 11320

East Asian (EAS) AF: 1.00 AC: 25739 AN: 25746

South Asian (SAS) AF: 0.841 AC: 23757 AN: 28238

European-Finnish (FIN) AF: 0.828 AC: 20652 AN: 24944

Middle Eastern (MID) AF: 0.891 AC: 1462 AN: 1640

European-Non Finnish (NFE) AF: 0.887 AC: 210016 AN: 236744

Other (OTH) AF: 0.884 AC: 19305 AN: 21828

GnomAD4 genome AF: 0.832 AC: 126250 AN: 151712 Hom.: 53348 Cov.: 31 AF XY: 0.831 AC XY: 61606 AN XY: 74134

African (AFR) AF: 0.680 AC: 28096 AN: 41332

American (AMR) AF: 0.902 AC: 13786 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3145 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5160

South Asian (SAS) AF: 0.854 AC: 4103 AN: 4806

European-Finnish (FIN) AF: 0.822 AC: 8631 AN: 10506

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60400 AN: 67854

Other (OTH) AF: 0.860 AC: 1812 AN: 2106

Alfa AF: 0.805 Hom.: 2790

Bravo AF: 0.835

Asia WGS AF: 0.926 AC: 3221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.9
DANN	Benign	0.58
PhyloP100		-0.48
PromoterAI		-0.12	Neutral
Mutation Taster		=300/0	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: rs1541254; hg19: chr1-203652140;