chr6-31970950-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005510.4(DXO):c.554T>C(p.Met185Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,613,034 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005510.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DXO | NM_005510.4 | c.554T>C | p.Met185Thr | missense_variant | 3/7 | ENST00000337523.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DXO | ENST00000337523.10 | c.554T>C | p.Met185Thr | missense_variant | 3/7 | 1 | NM_005510.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000513 AC: 78AN: 152194Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000122 AC: 30AN: 246438Hom.: 1 AF XY: 0.0000968 AC XY: 13AN XY: 134360
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1460722Hom.: 1 Cov.: 33 AF XY: 0.0000633 AC XY: 46AN XY: 726678
GnomAD4 genome ? AF: 0.000506 AC: 77AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.000564 AC XY: 42AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2023 | The c.554T>C (p.M185T) alteration is located in exon 3 (coding exon 2) of the DXO gene. This alteration results from a T to C substitution at nucleotide position 554, causing the methionine (M) at amino acid position 185 to be replaced by a threonine (T). 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