chr7-103300135-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004279.3(PMPCB):c.328-43T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 1,567,924 control chromosomes in the GnomAD database, including 1,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.049 ( 241 hom., cov: 33)
Exomes 𝑓: 0.035 ( 1066 hom. )
Consequence
PMPCB
NM_004279.3 intron
NM_004279.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.394
Genes affected
PMPCB (HGNC:9119): (peptidase, mitochondrial processing subunit beta) This gene is a member of the peptidase M16 family and encodes a protein with a zinc-binding motif. This protein is located in the mitochondrial matrix and catalyzes the cleavage of the leader peptides of precursor proteins newly imported into the mitochondria, though it only functions as part of a heterodimeric complex. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
?
Variant 7-103300135-T-C is Benign according to our data. Variant chr7-103300135-T-C is described in ClinVar as [Benign]. Clinvar id is 1281221.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0785 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMPCB | NM_004279.3 | c.328-43T>C | intron_variant | ENST00000249269.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMPCB | ENST00000249269.9 | c.328-43T>C | intron_variant | 1 | NM_004279.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0488 AC: 7431AN: 152130Hom.: 241 Cov.: 33
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GnomAD3 exomes AF: 0.0348 AC: 8291AN: 238046Hom.: 235 AF XY: 0.0332 AC XY: 4261AN XY: 128482
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GnomAD4 exome AF: 0.0348 AC: 49318AN: 1415676Hom.: 1066 Cov.: 23 AF XY: 0.0341 AC XY: 24096AN XY: 705976
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GnomAD4 genome ? AF: 0.0488 AC: 7431AN: 152248Hom.: 241 Cov.: 33 AF XY: 0.0490 AC XY: 3649AN XY: 74432
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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 | May 14, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at