chr6-55439475-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001042406.2(HMGCLL1):c.880G>A(p.Glu294Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000236 in 1,612,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001042406.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249106Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135162
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1460552Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726588
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.970G>A (p.E324K) alteration is located in exon 9 (coding exon 9) of the HMGCLL1 gene. This alteration results from a G to A substitution at nucleotide position 970, causing the glutamic acid (E) at amino acid position 324 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at