chrX-70200372-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_198512.3(DGAT2L6):c.385C>T(p.Arg129Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000169 in 1,210,000 control chromosomes in the GnomAD database, including 1 homozygotes. There are 65 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R129Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_198512.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGAT2L6 | NM_198512.3 | c.385C>T | p.Arg129Trp | missense_variant | 4/7 | ENST00000333026.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2L6 | ENST00000333026.4 | c.385C>T | p.Arg129Trp | missense_variant | 4/7 | 1 | NM_198512.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000867 AC: 97AN: 111884Hom.: 1 Cov.: 22 AF XY: 0.000939 AC XY: 32AN XY: 34090
GnomAD3 exomes AF: 0.000196 AC: 36AN: 183355Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67831
GnomAD4 exome AF: 0.0000984 AC: 108AN: 1098063Hom.: 0 Cov.: 31 AF XY: 0.0000881 AC XY: 32AN XY: 363421
GnomAD4 genome ? AF: 0.000867 AC: 97AN: 111937Hom.: 1 Cov.: 22 AF XY: 0.000966 AC XY: 33AN XY: 34153
ClinVar
Submissions by phenotype
DGAT2L6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 12, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at