NM_001037954.4:c.73G>C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001037954.4(DIXDC1):c.73G>C(p.Ala25Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000505 in 1,604,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIXDC1 | ENST00000440460.7 | c.73G>C | p.Ala25Pro | missense_variant | Exon 2 of 20 | 1 | NM_001037954.4 | ENSP00000394352.3 | ||
DIXDC1 | ENST00000529225.5 | c.70G>C | p.Ala24Pro | missense_variant | Exon 3 of 6 | 5 | ENSP00000434130.1 | |||
DIXDC1 | ENST00000528399.1 | n.153G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000256 AC: 6AN: 234562Hom.: 0 AF XY: 0.0000237 AC XY: 3AN XY: 126766
GnomAD4 exome AF: 0.0000537 AC: 78AN: 1451910Hom.: 0 Cov.: 30 AF XY: 0.0000499 AC XY: 36AN XY: 721138
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.73G>C (p.A25P) alteration is located in exon 2 (coding exon 2) of the DIXDC1 gene. This alteration results from a G to C substitution at nucleotide position 73, causing the alanine (A) at amino acid position 25 to be replaced by a proline (P). 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