chr16-84130356-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_031463.5(HSDL1):c.296G>A(p.Arg99Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,050 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R99W) has been classified as Uncertain significance.
Frequency
Consequence
NM_031463.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSDL1 | NM_031463.5 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 6 | ENST00000219439.9 | NP_113651.4 | |
HSDL1 | NM_001146051.2 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 7 | NP_001139523.1 | ||
HSDL1 | XM_005256189.4 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 6 | XP_005256246.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSDL1 | ENST00000219439.9 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 6 | 1 | NM_031463.5 | ENSP00000219439.4 | ||
HSDL1 | ENST00000434463.7 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 7 | 2 | ENSP00000407437.3 | |||
HSDL1 | ENST00000568857.5 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 4 | 4 | ENSP00000457026.1 | |||
HSDL1 | ENST00000562224.1 | c.296G>A | p.Arg99Gln | missense_variant | Exon 4 of 4 | 4 | ENSP00000455797.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251462Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135906
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727238
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.296G>A (p.R99Q) alteration is located in exon 4 (coding exon 2) of the HSDL1 gene. This alteration results from a G to A substitution at nucleotide position 296, causing the arginine (R) at amino acid position 99 to be replaced by a glutamine (Q). 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