1-1312208-G-C
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017871.6(INTS11):c.1607+18C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000085 ( 0 hom., cov: 20)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
INTS11
NM_017871.6 intron
NM_017871.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0330
Genes affected
INTS11 (HGNC:26052): (integrator complex subunit 11) The Integrator complex contains at least 12 subunits and associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates the 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690). INTS11, or CPSF3L, is the catalytic subunit of the Integrator complex (Baillat et al., 2005 [PubMed 16239144]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000850 AC: 1AN: 117608Hom.: 0 Cov.: 20
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GnomAD3 exomes AF: 0.00000939 AC: 1AN: 106506Hom.: 0 AF XY: 0.0000177 AC XY: 1AN XY: 56340
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GnomAD4 exome AF: 0.0000109 AC: 11AN: 1005604Hom.: 0 Cov.: 18 AF XY: 0.0000181 AC XY: 9AN XY: 497628
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GnomAD4 genome AF: 0.00000849 AC: 1AN: 117748Hom.: 0 Cov.: 20 AF XY: 0.0000175 AC XY: 1AN XY: 57042
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ClinVar
Not reported inComputational scores
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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