X-70177608-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_198512.3(DGAT2L6):āc.26T>Cā(p.Leu9Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000331 in 1,209,405 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_198512.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DGAT2L6 | NM_198512.3 | c.26T>C | p.Leu9Pro | missense_variant | 1/7 | ENST00000333026.4 | NP_940914.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DGAT2L6 | ENST00000333026.4 | c.26T>C | p.Leu9Pro | missense_variant | 1/7 | 1 | NM_198512.3 | ENSP00000328036.3 |
Frequencies
GnomAD3 genomes AF: 0.00000892 AC: 1AN: 112073Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34281
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097332Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 362724
GnomAD4 genome AF: 0.00000892 AC: 1AN: 112073Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34281
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2024 | The c.26T>C (p.L9P) alteration is located in exon 1 (coding exon 1) of the DGAT2L6 gene. This alteration results from a T to C substitution at nucleotide position 26, causing the leucine (L) at amino acid position 9 to be replaced by a proline (P). 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