chrX-70200373-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198512.3(DGAT2L6):c.386G>A(p.Arg129Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 1,210,021 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R129W) has been classified as Likely benign.
Frequency
Consequence
NM_198512.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGAT2L6 | NM_198512.3 | c.386G>A | p.Arg129Gln | missense_variant | 4/7 | ENST00000333026.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2L6 | ENST00000333026.4 | c.386G>A | p.Arg129Gln | missense_variant | 4/7 | 1 | NM_198512.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000268 AC: 3AN: 111876Hom.: 0 Cov.: 23 AF XY: 0.0000587 AC XY: 2AN XY: 34062
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183353Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67825
GnomAD4 exome AF: 0.00000546 AC: 6AN: 1098094Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 3AN XY: 363454
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111927Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34123
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.386G>A (p.R129Q) alteration is located in exon 4 (coding exon 4) of the DGAT2L6 gene. This alteration results from a G to A substitution at nucleotide position 386, causing the arginine (R) at amino acid position 129 to be replaced by a glutamine (Q). 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