chrX-50391446-A-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001013742.4(DGKK):c.1835T>A(p.Ile612Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00333 in 1,209,523 control chromosomes in the GnomAD database, including 96 homozygotes. There are 1,079 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 49 hom., 541 hem., cov: 23)
Exomes 𝑓: 0.0019 ( 47 hom. 538 hem. )
Consequence
DGKK
NM_001013742.4 missense
NM_001013742.4 missense
Scores
1
2
7
Clinical Significance
Conservation
PhyloP100: 5.17
Genes affected
DGKK (HGNC:32395): (diacylglycerol kinase kappa) The protein encoded by this gene is an enzyme that phosphorylates diacylglycerol, converting it to phosphatidic acid. The encoded protein is a membrane protein and is inhibited by hydrogen peroxide. Variations in this gene have been associated with hypospadias. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0054518282).
BP6
Variant X-50391446-A-T is Benign according to our data. Variant chrX-50391446-A-T is described in ClinVar as [Benign]. Clinvar id is 785700.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DGKK | NM_001013742.4 | c.1835T>A | p.Ile612Asn | missense_variant | 11/28 | ENST00000611977.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DGKK | ENST00000611977.2 | c.1835T>A | p.Ile612Asn | missense_variant | 11/28 | 1 | NM_001013742.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2001AN: 111939Hom.: 49 Cov.: 23 AF XY: 0.0159 AC XY: 544AN XY: 34117
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GnomAD3 exomes AF: 0.00474 AC: 857AN: 180875Hom.: 21 AF XY: 0.00342 AC XY: 229AN XY: 66965
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GnomAD4 exome AF: 0.00185 AC: 2034AN: 1097530Hom.: 47 Cov.: 30 AF XY: 0.00148 AC XY: 538AN XY: 363168
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GnomAD4 genome AF: 0.0178 AC: 1998AN: 111993Hom.: 49 Cov.: 23 AF XY: 0.0158 AC XY: 541AN XY: 34181
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
PrimateAI
Uncertain
T
Sift4G
Uncertain
D
Polyphen
P
Vest4
MVP
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Splicing
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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