chr4-108014612-CT-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_005327.7(HADH):c.419+39delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 145,440 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_005327.7 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HADH | NM_005327.7 | c.419+39delT | intron_variant | Intron 3 of 7 | ENST00000309522.8 | NP_005318.6 | ||
HADH | NM_001184705.4 | c.419+39delT | intron_variant | Intron 3 of 8 | NP_001171634.3 | |||
HADH | NM_001331027.2 | c.431+39delT | intron_variant | Intron 3 of 7 | NP_001317956.2 | |||
HADH | XR_007096395.1 | n.463+39delT | intron_variant | Intron 3 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00316 AC: 459AN: 145380Hom.: 2 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.231 AC: 190128AN: 824632Hom.: 165 Cov.: 0 AF XY: 0.238 AC XY: 95865AN XY: 403542
GnomAD4 genome AF: 0.00316 AC: 460AN: 145440Hom.: 2 Cov.: 32 AF XY: 0.00341 AC XY: 241AN XY: 70618
ClinVar
Submissions by phenotype
Hyperinsulinemic hypoglycemia Uncertain:1
Potent mutations in HADH gene are associated with congenital hyperinsulinism, which leads to recurrent hypoglycemia. The condition is exacerbated by stress, fasting or excessive dietary protein. May respond well to diazoxide. However, the role of this particular variant rs550348868 in congenital hyperinsulinism is yet to be ascertained. -
not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at