6-55435732-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001042406.2(HMGCLL1):c.953G>T(p.Gly318Val) variant causes a missense change. The variant allele was found at a frequency of 0.00002 in 1,603,102 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: 0.0000987 AC: 15AN: 151904Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242456Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131928
GnomAD4 exome AF: 0.0000117 AC: 17AN: 1451198Hom.: 0 Cov.: 28 AF XY: 0.0000139 AC XY: 10AN XY: 721784
GnomAD4 genome AF: 0.0000987 AC: 15AN: 151904Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1043G>T (p.G348V) alteration is located in exon 10 (coding exon 10) of the HMGCLL1 gene. This alteration results from a G to T substitution at nucleotide position 1043, causing the glycine (G) at amino acid position 348 to be replaced by a valine (V). 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