4-113049622-A-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000506722.5(ANK2):c.22-124794A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000446 in 1,216,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00045 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ANK2
ENST00000506722.5 intron
ENST00000506722.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.659
Genes affected
ANK2 (HGNC:493): (ankyrin 2) This gene encodes a member of the ankyrin family of proteins that link the integral membrane proteins to the underlying spectrin-actin cytoskeleton. Ankyrins play key roles in activities such as cell motility, activation, proliferation, contact and the maintenance of specialized membrane domains. Most ankyrins are typically composed of three structural domains: an amino-terminal domain containing multiple ankyrin repeats; a central region with a highly conserved spectrin binding domain; and a carboxy-terminal regulatory domain which is the least conserved and subject to variation. The protein encoded by this gene is required for targeting and stability of Na/Ca exchanger 1 in cardiomyocytes. Mutations in this gene cause long QT syndrome 4 and cardiac arrhythmia syndrome. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 4-113049622-A-C is Benign according to our data. Variant chr4-113049622-A-C is described in ClinVar as [Benign]. Clinvar id is 1292223.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAdExome4 at 542 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANK2 | NM_001148.6 | upstream_gene_variant | ENST00000357077.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANK2-AS1 | ENST00000508959.1 | n.126-14828T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
ANK2 | ENST00000357077.9 | upstream_gene_variant | 1 | NM_001148.6 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 146890Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome AF: 0.000446 AC: 542AN: 1216030Hom.: 0 Cov.: 31 AF XY: 0.000468 AC XY: 281AN XY: 599844
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000136 AC: 2AN: 147010Hom.: 0 Cov.: 32 AF XY: 0.0000140 AC XY: 1AN XY: 71430
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.