rs10795122
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000280886.12(DIP2C):c.605-1691T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,020 control chromosomes in the GnomAD database, including 11,018 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 0.35 ( 11018 hom., cov: 32)
Consequence
DIP2C
ENST00000280886.12 intron
ENST00000280886.12 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.687
Genes affected
DIP2C (HGNC:29150): (disco interacting protein 2 homolog C) This gene encodes a member of the disco-interacting protein homolog 2 family. The protein shares strong similarity with a Drosophila protein which interacts with the transcription factor disco and is expressed in the nervous system. [provided by RefSeq, Oct 2008]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIP2C | NM_014974.3 | c.605-1691T>C | intron_variant | ENST00000280886.12 | NP_055789.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DIP2C | ENST00000280886.12 | c.605-1691T>C | intron_variant | 1 | NM_014974.3 | ENSP00000280886 | P1 | |||
DIP2C | ENST00000634311.1 | c.773-1691T>C | intron_variant | 5 | ENSP00000489203 |
Frequencies
GnomAD3 genomes AF: 0.355 AC: 53885AN: 151902Hom.: 11007 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.355 AC: 53908AN: 152020Hom.: 11018 Cov.: 32 AF XY: 0.351 AC XY: 26047AN XY: 74290
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1188
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3478
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at