9-113374258-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001304509.2(HDHD3):c.97G>A(p.Ala33Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000163 in 1,598,700 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001304509.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDHD3 | ENST00000374180.4 | c.97G>A | p.Ala33Thr | missense_variant | Exon 3 of 3 | 1 | NM_001304509.2 | ENSP00000363295.3 | ||
HDHD3 | ENST00000238379.9 | c.97G>A | p.Ala33Thr | missense_variant | Exon 2 of 2 | 1 | ENSP00000238379.5 | |||
HDHD3 | ENST00000485934.1 | n.543G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000837 AC: 20AN: 238948Hom.: 0 AF XY: 0.0000696 AC XY: 9AN XY: 129252
GnomAD4 exome AF: 0.000173 AC: 250AN: 1446496Hom.: 0 Cov.: 33 AF XY: 0.000169 AC XY: 121AN XY: 717634
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.97G>A (p.A33T) alteration is located in exon 2 (coding exon 1) of the HDHD3 gene. This alteration results from a G to A substitution at nucleotide position 97, causing the alanine (A) at amino acid position 33 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