rs758109052
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_152363.6(ANKLE1):c.*140_*143del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 902,542 control chromosomes in the GnomAD database, including 3,277 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 1866 hom., cov: 0)
Exomes 𝑓: 0.17 ( 1411 hom. )
Consequence
ANKLE1
NM_152363.6 3_prime_UTR
NM_152363.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.273
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 -10 ACMG points.
BP6
?
Variant 19-17286688-GTGTT-G is Benign according to our data. Variant chr19-17286688-GTGTT-G is described in ClinVar as [Benign]. Clinvar id is 402369.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKLE1 | NM_152363.6 | c.*140_*143del | 3_prime_UTR_variant | 9/9 | ENST00000404085.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKLE1 | ENST00000404085.7 | c.*140_*143del | 3_prime_UTR_variant | 9/9 | 2 | NM_152363.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.224 AC: 22635AN: 100914Hom.: 1860 Cov.: 0
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GnomAD3 exomes AF: 0.134 AC: 8740AN: 65312Hom.: 160 AF XY: 0.132 AC XY: 4485AN XY: 33936
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GnomAD4 exome AF: 0.167 AC: 133631AN: 801554Hom.: 1411 AF XY: 0.170 AC XY: 65720AN XY: 386214
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GnomAD4 genome ? AF: 0.224 AC: 22650AN: 100988Hom.: 1866 Cov.: 0 AF XY: 0.219 AC XY: 10750AN XY: 49104
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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 - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at