3-123502648-T-C
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_198402.5(HACD2):c.415A>G(p.Ile139Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,605,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198402.5 missense
Scores
Clinical Significance
Conservation
Publications
Genome browser will be placed here
ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HACD2 | ENST00000383657.10 | c.415A>G | p.Ile139Val | missense_variant | Exon 5 of 7 | 1 | NM_198402.5 | ENSP00000373153.5 | ||
HACD2 | ENST00000469317.1 | c.82A>G | p.Ile28Val | missense_variant | Exon 5 of 6 | 3 | ENSP00000419237.1 | |||
HACD2 | ENST00000480081.1 | n.259A>G | non_coding_transcript_exon_variant | Exon 1 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151902Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000509 AC: 12AN: 235970 AF XY: 0.0000471 show subpopulations
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1453862Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 722194 show subpopulations
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74276 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.415A>G (p.I139V) alteration is located in exon 5 (coding exon 5) of the HACD2 gene. This alteration results from a A to G substitution at nucleotide position 415, causing the isoleucine (I) at amino acid position 139 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