chr16-89508295-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The XR_007065184.1(LOC101927863):n.41T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000658 in 909,792 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0026 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00027 ( 0 hom. )
Consequence
LOC101927863
XR_007065184.1 non_coding_transcript_exon
XR_007065184.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0230
Genes affected
SPG7 (HGNC:11237): (SPG7 matrix AAA peptidase subunit, paraplegin) This gene encodes a mitochondrial metalloprotease protein that is a member of the AAA family. Members of this protein family share an ATPase domain and have roles in diverse cellular processes including membrane trafficking, intracellular motility, organelle biogenesis, protein folding, and proteolysis. Mutations in this gene cause autosomal recessive spastic paraplegia 7. Two transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Mar 2014]
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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=-0.82).
BP6
?
Variant 16-89508295-A-C is Benign according to our data. Variant chr16-89508295-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1209194.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC101927863 | XR_007065184.1 | n.41T>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPG7 | ENST00000646303.1 | c.51+555A>C | intron_variant | ||||||
SPG7 | ENST00000647079.1 | c.-225-2195A>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00262 AC: 398AN: 151986Hom.: 5 Cov.: 33
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GnomAD4 exome AF: 0.000265 AC: 201AN: 757694Hom.: 0 Cov.: 10 AF XY: 0.000248 AC XY: 91AN XY: 366992
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GnomAD4 genome ? AF: 0.00262 AC: 398AN: 152098Hom.: 5 Cov.: 33 AF XY: 0.00246 AC XY: 183AN XY: 74360
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2018 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at