chr10-87862147-CCT-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001126049.2(KLLN):c.339_340delAG(p.Ala115SerfsTer58) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,550,696 control chromosomes in the GnomAD database, including 9 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001126049.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00165 AC: 251AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00141 AC: 215AN: 152990Hom.: 2 AF XY: 0.00135 AC XY: 110AN XY: 81306
GnomAD4 exome AF: 0.00233 AC: 3254AN: 1398504Hom.: 9 AF XY: 0.00227 AC XY: 1568AN XY: 689690
GnomAD4 genome AF: 0.00165 AC: 251AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00161 AC XY: 120AN XY: 74344
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
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not specified Uncertain:2
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KLLN-related disorder Benign:1
This variant is classified as likely 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