chr6-55541742-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001042406.2(HMGCLL1):āc.284G>Cā(p.Arg95Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000909 in 1,584,954 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R95I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001042406.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMGCLL1 | NM_001042406.2 | c.284G>C | p.Arg95Thr | missense_variant | 3/9 | ENST00000274901.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGCLL1 | ENST00000274901.9 | c.284G>C | p.Arg95Thr | missense_variant | 3/9 | 1 | NM_001042406.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 17AN: 235154Hom.: 0 AF XY: 0.0000784 AC XY: 10AN XY: 127492
GnomAD4 exome AF: 0.0000789 AC: 113AN: 1432862Hom.: 0 Cov.: 27 AF XY: 0.0000785 AC XY: 56AN XY: 713388
GnomAD4 genome AF: 0.000204 AC: 31AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | The c.374G>C (p.R125T) alteration is located in exon 4 (coding exon 4) of the HMGCLL1 gene. This alteration results from a G to C substitution at nucleotide position 374, causing the arginine (R) at amino acid position 125 to be replaced by a threonine (T). 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