14-50247222-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024884.3(L2HGDH):c.1228G>A(p.Asp410Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,613,910 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_024884.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
L2HGDH | ENST00000267436.9 | c.1228G>A | p.Asp410Asn | missense_variant | Exon 10 of 10 | 1 | NM_024884.3 | ENSP00000267436.4 | ||
L2HGDH | ENST00000261699.8 | c.1197-9497G>A | intron_variant | Intron 9 of 9 | 1 | ENSP00000261699.4 | ||||
L2HGDH | ENST00000421284.7 | c.1228G>A | p.Asp410Asn | missense_variant | Exon 10 of 11 | 2 | ENSP00000405559.3 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250672Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135536
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461710Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727138
GnomAD4 genome AF: 0.000138 AC: 21AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Inborn genetic diseases Uncertain:1
The c.1228G>A (p.D410N) alteration is located in exon 10 (coding exon 10) of the L2HGDH gene. This alteration results from a G to A substitution at nucleotide position 1228, causing the aspartic acid (D) at amino acid position 410 to be replaced by an asparagine (N). 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