Variant rs13076493 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378511.1(ATP2C1):c.2857-4479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,112 control chromosomes in the GnomAD database, including 3,816 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 0.22 ( 3816 hom., cov: 32)

Consequence

ATP2C1
NM_001378511.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.181

Variant links:

Genes affected

ATP2C1 (HGNC:13211): (ATPase secretory pathway Ca2+ transporting 1) The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium ions. Defects in this gene cause Hailey-Hailey disease, an autosomal dominant disorder. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

ATP2C1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
ATP2C1	NM_001378511.1 link	c.2857-4479C>T	intron_variant	NP_001365440.1
ATP2C1	NM_001199180.2 link	c.2827-4479C>T	intron_variant	NP_001186109.1	P98194-7
ATP2C1	NM_001001486.2 link	c.2755-4479C>T	intron_variant	NP_001001486.1	P98194-9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
ATP2C1	ENST00000359644.7 link	c.2755-4479C>T	intron_variant	1	ENSP00000352665.3	P98194-9
ATP2C1	ENST00000422190.6 link	c.2725-4479C>T	intron_variant	1	ENSP00000402677.2	P98194-5
ATP2C1	ENST00000513801.5 link	c.2677-4479C>T	intron_variant	1	ENSP00000422872.1	P98194-3

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33187

AN:

151994

Hom.:

3813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.149

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.221

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

GnomAD4 genome

AF:

0.218

AC:

33219

AN:

152112

Hom.:

3816

Cov.:

AF XY:

0.212

AC XY:

15730

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.158

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.220

Gnomad4 FIN

AF:

0.149

Gnomad4 NFE

AF:

0.213

Gnomad4 OTH

AF:

0.222

Alfa

AF:

0.222

Hom.:

854

Bravo

AF:

0.223

Asia WGS

AF:

0.181

AC:

633

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.9

DANN

Benign

0.48

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over