rs650461
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001037954.4(DIXDC1):c.1972-45C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,535,612 control chromosomes in the GnomAD database, including 132,460 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.50 ( 21444 hom., cov: 32)
Exomes 𝑓: 0.39 ( 111016 hom. )
Consequence
DIXDC1
NM_001037954.4 intron
NM_001037954.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.838
Genes affected
DIXDC1 (HGNC:23695): (DIX domain containing 1) The protein encoded by this gene is a positive regulator of the Wnt signaling pathway. The encoded protein is found associated with gamma tubulin at the centrosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIXDC1 | NM_001037954.4 | c.1972-45C>G | intron_variant | ENST00000440460.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIXDC1 | ENST00000440460.7 | c.1972-45C>G | intron_variant | 1 | NM_001037954.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.501 AC: 76070AN: 151972Hom.: 21390 Cov.: 32
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GnomAD3 exomes AF: 0.430 AC: 104580AN: 243088Hom.: 23920 AF XY: 0.420 AC XY: 55571AN XY: 132170
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GnomAD4 exome AF: 0.393 AC: 543995AN: 1383522Hom.: 111016 Cov.: 20 AF XY: 0.393 AC XY: 272126AN XY: 692988
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GnomAD4 genome ? AF: 0.501 AC: 76182AN: 152090Hom.: 21444 Cov.: 32 AF XY: 0.504 AC XY: 37462AN XY: 74314
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at