chr11-111974104-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001037954.4(DIXDC1):c.398C>T(p.Thr133Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037954.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIXDC1 | NM_001037954.4 | c.398C>T | p.Thr133Met | missense_variant | 4/20 | ENST00000440460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIXDC1 | ENST00000440460.7 | c.398C>T | p.Thr133Met | missense_variant | 4/20 | 1 | NM_001037954.4 | P1 | |
DIXDC1 | ENST00000529225.5 | c.395C>T | p.Thr132Met | missense_variant | 5/6 | 5 | |||
DIXDC1 | ENST00000528399.1 | n.478C>T | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249244Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135216
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461680Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727116
GnomAD4 genome AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2021 | The c.398C>T (p.T133M) alteration is located in exon 4 (coding exon 4) of the DIXDC1 gene. This alteration results from a C to T substitution at nucleotide position 398, causing the threonine (T) at amino acid position 133 to be replaced by a methionine (M). 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