chr19-17286684-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152363.6(ANKLE1):c.*132G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,012,124 control chromosomes in the GnomAD database, including 1,458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 565 hom., cov: 26)
Exomes 𝑓: 0.13 ( 893 hom. )
Consequence
ANKLE1
NM_152363.6 3_prime_UTR
NM_152363.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.223
Genes affected
ANKLE1 (HGNC:26812): (ankyrin repeat and LEM domain containing 1) Enables endonuclease activity. Involved in positive regulation of response to DNA damage stimulus and protein export from nucleus. Located in cytosol and nucleoplasm. Colocalizes with nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 19-17286684-G-T is Benign according to our data. Variant chr19-17286684-G-T is described in ClinVar as [Benign]. Clinvar id is 402368.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKLE1 | NM_152363.6 | c.*132G>T | 3_prime_UTR_variant | 9/9 | ENST00000404085.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKLE1 | ENST00000404085.7 | c.*132G>T | 3_prime_UTR_variant | 9/9 | 2 | NM_152363.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.102 AC: 11660AN: 114518Hom.: 562 Cov.: 26
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GnomAD3 exomes AF: 0.0805 AC: 5869AN: 72870Hom.: 119 AF XY: 0.0801 AC XY: 3057AN XY: 38158
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GnomAD4 exome AF: 0.129 AC: 116096AN: 897520Hom.: 893 Cov.: 28 AF XY: 0.128 AC XY: 55880AN XY: 438002
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GnomAD4 genome AF: 0.102 AC: 11667AN: 114604Hom.: 565 Cov.: 26 AF XY: 0.0987 AC XY: 5505AN XY: 55762
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside ROI, Frequency - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at