7-1470934-G-A
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001080453.3(INTS1):c.6369C>T(p.Pro2123=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000703 in 1,422,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000070 ( 0 hom. )
Consequence
INTS1
NM_001080453.3 synonymous
NM_001080453.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.420
Genes affected
INTS1 (HGNC:24555): (integrator complex subunit 1) INTS1 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (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 -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 7-1470934-G-A is Benign according to our data. Variant chr7-1470934-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3352535.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS1 | NM_001080453.3 | c.6369C>T | p.Pro2123= | synonymous_variant | 47/48 | ENST00000404767.8 | |
INTS1 | XM_011515260.2 | c.6399C>T | p.Pro2133= | synonymous_variant | 47/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS1 | ENST00000404767.8 | c.6369C>T | p.Pro2123= | synonymous_variant | 47/48 | 5 | NM_001080453.3 | P1 | |
INTS1 | ENST00000493446.1 | n.353C>T | non_coding_transcript_exon_variant | 5/6 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183566Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 99030
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GnomAD4 exome AF: 0.00000703 AC: 10AN: 1422124Hom.: 0 Cov.: 31 AF XY: 0.00000426 AC XY: 3AN XY: 703936
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
INTS1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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