chr19-5711908-CCTT-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PM4_SupportingBP6_Very_StrongBS2
The NM_004793.4(LONP1):c.730_732delAAG(p.Lys244del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.000614 in 1,613,192 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004793.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00346 AC: 527AN: 152192Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000886 AC: 222AN: 250704Hom.: 1 AF XY: 0.000811 AC XY: 110AN XY: 135676
GnomAD4 exome AF: 0.000317 AC: 463AN: 1460882Hom.: 2 AF XY: 0.000308 AC XY: 224AN XY: 726832
GnomAD4 genome AF: 0.00347 AC: 528AN: 152310Hom.: 2 Cov.: 32 AF XY: 0.00334 AC XY: 249AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:3
LONP1: PM4:Supporting, BS1, BS2 -
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LONP1-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at