7-1471218-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001080453.3(INTS1):c.6262C>T(p.Leu2088=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000734 in 1,577,004 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 (★).
Frequency
Genomes: 𝑓 0.00067 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00074 ( 0 hom. )
Consequence
INTS1
NM_001080453.3 synonymous
NM_001080453.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.22
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 -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 7-1471218-G-A is Benign according to our data. Variant chr7-1471218-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3234163.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-1471218-G-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=3.22 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INTS1 | NM_001080453.3 | c.6262C>T | p.Leu2088= | synonymous_variant | 46/48 | ENST00000404767.8 | |
INTS1 | XM_011515260.2 | c.6292C>T | p.Leu2098= | synonymous_variant | 46/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INTS1 | ENST00000404767.8 | c.6262C>T | p.Leu2088= | synonymous_variant | 46/48 | 5 | NM_001080453.3 | P1 | |
INTS1 | ENST00000483196.1 | c.301C>T | p.Leu101= | synonymous_variant | 4/4 | 5 | |||
INTS1 | ENST00000479671.1 | n.198C>T | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
INTS1 | ENST00000493446.1 | n.246C>T | non_coding_transcript_exon_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000670 AC: 102AN: 152258Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000492 AC: 91AN: 184846Hom.: 0 AF XY: 0.000471 AC XY: 47AN XY: 99728
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GnomAD4 exome AF: 0.000740 AC: 1055AN: 1424746Hom.: 0 Cov.: 31 AF XY: 0.000742 AC XY: 523AN XY: 705256
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GnomAD4 genome AF: 0.000670 AC: 102AN: 152258Hom.: 0 Cov.: 34 AF XY: 0.000605 AC XY: 45AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | INTS1: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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