chrX-70199359-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_198512.3(DGAT2L6):c.174T>C(p.Tyr58=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000447 in 1,185,809 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., 11 hem., cov: 22)
Exomes 𝑓: 0.000029 ( 0 hom. 6 hem. )
Consequence
DGAT2L6
NM_198512.3 synonymous
NM_198512.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.308
Genes affected
DGAT2L6 (HGNC:23250): (diacylglycerol O-acyltransferase 2 like 6) This gene is a member of the diacylglycerol acyltransferase 2 family. The encoded protein is a putative acyltransferase and is most likely involved in the synthesis of di- or triacylglycerol, however its substrate specificity is currently unknown. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant X-70199359-T-C is Benign according to our data. Variant chrX-70199359-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3052464.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.308 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd at 11 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGAT2L6 | NM_198512.3 | c.174T>C | p.Tyr58= | synonymous_variant | 2/7 | ENST00000333026.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGAT2L6 | ENST00000333026.4 | c.174T>C | p.Tyr58= | synonymous_variant | 2/7 | 1 | NM_198512.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000198 AC: 22AN: 110989Hom.: 0 Cov.: 22 AF XY: 0.000331 AC XY: 11AN XY: 33235
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GnomAD3 exomes AF: 0.0000816 AC: 12AN: 147076Hom.: 0 AF XY: 0.0000670 AC XY: 3AN XY: 44754
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GnomAD4 exome AF: 0.0000288 AC: 31AN: 1074771Hom.: 0 Cov.: 29 AF XY: 0.0000173 AC XY: 6AN XY: 347593
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GnomAD4 genome ? AF: 0.000198 AC: 22AN: 111038Hom.: 0 Cov.: 22 AF XY: 0.000330 AC XY: 11AN XY: 33294
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DGAT2L6-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 05, 2019 | 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
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at