rs962782746

Variant names:

• chr1-160128857-G-T
• rs962782746
• NM_000702.4:c.1216+7G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_000702.4(ATP1A2):​c.1216+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: ATP1A2 NM_000702.4 splice_region, intron
• Scores: Splicing: ADA: 0.02254
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.55
• Publications: 0 publications found

Genes affected

ATP1A2 (HGNC:800): (ATPase Na+/K+ transporting subunit alpha 2) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 2 subunit. Mutations in this gene result in familial basilar or hemiplegic migraines, and in a rare syndrome known as alternating hemiplegia of childhood. [provided by RefSeq, Oct 2008]

ATP1A2 Gene-Disease associations (from GenCC):

• hemiplegic migraine-developmental and epileptic encephalopathy spectrum

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• migraine, familial hemiplegic, 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• alternating hemiplegia of childhood 1

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• developmental and epileptic encephalopathy 98

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic facies

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
• alternating hemiplegia of childhood

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial or sporadic hemiplegic migraine

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.156).
• BP6: Variant 1-160128857-G-T is Benign according to our data. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-160128857-G-T is described in CliVar as Likely_benign. Clinvar id is 529758.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP1A2	NM_000702.4	c.1216+7G>T		splice_region_variant, intron_variant	Intron 9 of 22	ENST00000361216.8	NP_000693.1
ATP1A2	XM_047421286.1	c.325+7G>T		splice_region_variant, intron_variant	Intron 2 of 15		XP_047277242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP1A2	ENST00000361216.8	c.1216+7G>T		splice_region_variant, intron_variant	Intron 9 of 22	1	NM_000702.4	ENSP00000354490.3
ATP1A2	ENST00000392233.7	c.1216+7G>T		splice_region_variant, intron_variant	Intron 9 of 22	5		ENSP00000376066.3
ATP1A2	ENST00000447527.1	c.346+7G>T		splice_region_variant, intron_variant	Intron 2 of 15	2		ENSP00000411705.1
ATP1A2	ENST00000472488.5	n.1319+7G>T		splice_region_variant, intron_variant	Intron 9 of 19	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1461858 Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2 AN XY: 727228

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000360 AC: 4 AN: 1111994

Other (OTH) AF: 0.00 AC: 0 AN: 60394

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial hemiplegic migraine Benign:1

Oct 22, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	14
DANN	Benign	0.97
PhyloP100		2.6

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.023
dbscSNV1_RF	Benign	0.20
SpliceAI score (max)		0.090		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: rs962782746; hg19: chr1-160098647;