rs10209401
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_026597.2(DIRC3):n.2291-11806T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,072 control chromosomes in the GnomAD database, including 46,623 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 0.76 ( 46623 hom., cov: 30)
Consequence
DIRC3
NR_026597.2 intron, non_coding_transcript
NR_026597.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.669
Genes affected
DIRC3 (HGNC:17805): (disrupted in renal carcinoma 3)
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DIRC3 | NR_026597.2 | n.2291-11806T>G | intron_variant, non_coding_transcript_variant | ||||
DIRC3-AS1 | NR_133642.1 | n.1024+3377A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DIRC3 | ENST00000486365.5 | n.2291-11806T>G | intron_variant, non_coding_transcript_variant | 5 | |||||
DIRC3 | ENST00000474063.5 | n.1459-11806T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
DIRC3 | ENST00000663562.1 | n.2378-11806T>G | intron_variant, non_coding_transcript_variant | ||||||
DIRC3 | ENST00000676082.1 | n.1041-11806T>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.764 AC: 116089AN: 151954Hom.: 46613 Cov.: 30
GnomAD3 genomes
?
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151954
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.764 AC: 116133AN: 152072Hom.: 46623 Cov.: 30 AF XY: 0.766 AC XY: 56918AN XY: 74334
GnomAD4 genome
?
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116133
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30
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56918
AN XY:
74334
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2371
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at