15-89333596-TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGC-TTGCTGCTGCTGCTGCTGCTGCTGCTGC
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP3BP6_Very_StrongBS2
The NM_001430120.1(POLGARF):c.211_213delGCA(p.Ala71del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,579,960 control chromosomes in the GnomAD database, including 92 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001430120.1 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLG | NM_002693.3 | c.156_158delGCA | p.Gln53del | disruptive_inframe_deletion | Exon 2 of 23 | ENST00000268124.11 | NP_002684.1 | |
POLGARF | NM_001430120.1 | c.211_213delGCA | p.Ala71del | conservative_inframe_deletion | Exon 1 of 2 | NP_001417049.1 | ||
POLG | NM_001126131.2 | c.156_158delGCA | p.Gln53del | disruptive_inframe_deletion | Exon 2 of 23 | NP_001119603.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLGARF | ENST00000706918.1 | c.211_213delGCA | p.Ala71del | conservative_inframe_deletion | Exon 1 of 2 | ENSP00000516626.1 | ||||
POLG | ENST00000268124.11 | c.156_158delGCA | p.Gln53del | disruptive_inframe_deletion | Exon 2 of 23 | 1 | NM_002693.3 | ENSP00000268124.5 |
Frequencies
GnomAD3 genomes AF: 0.00902 AC: 1367AN: 151586Hom.: 5 Cov.: 30
GnomAD4 exome AF: 0.0111 AC: 15824AN: 1428270Hom.: 87 AF XY: 0.0110 AC XY: 7817AN XY: 709892
GnomAD4 genome AF: 0.00902 AC: 1369AN: 151690Hom.: 5 Cov.: 30 AF XY: 0.00933 AC XY: 692AN XY: 74152
ClinVar
Submissions by phenotype
not specified Benign:7
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The variant is found in EPILEPSY,CHILD-EPI,MITONUC-MITOP panel(s). -
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not provided Benign:3
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POLG: BS1, BS2 -
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Hereditary spastic paraplegia Benign:1
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POLG-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Progressive sclerosing poliodystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at