chr17-45445409-TTGTG-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_014798.3(PLEKHM1):c.2837+57_2837+60del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 1,407,996 control chromosomes in the GnomAD database, including 15,833 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.13 ( 1431 hom., cov: 30)
Exomes 𝑓: 0.16 ( 14402 hom. )
Consequence
PLEKHM1
NM_014798.3 intron
NM_014798.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.01
Genes affected
PLEKHM1 (HGNC:29017): (pleckstrin homology and RUN domain containing M1) The protein encoded by this gene is essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 17-45445409-TTGTG-T is Benign according to our data. Variant chr17-45445409-TTGTG-T is described in ClinVar as [Benign]. Clinvar id is 1259474.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHM1 | NM_014798.3 | c.2837+57_2837+60del | intron_variant | ENST00000430334.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHM1 | ENST00000430334.8 | c.2837+57_2837+60del | intron_variant | 1 | NM_014798.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.127 AC: 19215AN: 151718Hom.: 1433 Cov.: 30
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GnomAD4 exome AF: 0.157 AC: 197165AN: 1256160Hom.: 14402 AF XY: 0.155 AC XY: 98015AN XY: 633256
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GnomAD4 genome ? AF: 0.127 AC: 19212AN: 151836Hom.: 1431 Cov.: 30 AF XY: 0.119 AC XY: 8835AN XY: 74280
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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 | Nov 12, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at