6-55495430-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001042406.2(HMGCLL1):c.784A>T(p.Thr262Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,408 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T262M) 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.784A>T | p.Thr262Ser | missense_variant | 7/9 | ENST00000274901.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGCLL1 | ENST00000274901.9 | c.784A>T | p.Thr262Ser | missense_variant | 7/9 | 1 | NM_001042406.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248832Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135034
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461250Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726950
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.874A>T (p.T292S) alteration is located in exon 8 (coding exon 8) of the HMGCLL1 gene. This alteration results from a A to T substitution at nucleotide position 874, causing the threonine (T) at amino acid position 292 to be replaced by a serine (S). 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