7-1471218-G-A

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.22
Variant links:
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]

Genome browser will be placed here

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
INTS1NM_001080453.3 linkuse as main transcriptc.6262C>T p.Leu2088= synonymous_variant 46/48 ENST00000404767.8
INTS1XM_011515260.2 linkuse as main transcriptc.6292C>T p.Leu2098= synonymous_variant 46/48

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
INTS1ENST00000404767.8 linkuse as main transcriptc.6262C>T p.Leu2088= synonymous_variant 46/485 NM_001080453.3 P1
INTS1ENST00000483196.1 linkuse as main transcriptc.301C>T p.Leu101= synonymous_variant 4/45
INTS1ENST00000479671.1 linkuse as main transcriptn.198C>T non_coding_transcript_exon_variant 2/22
INTS1ENST00000493446.1 linkuse as main transcriptn.246C>T non_coding_transcript_exon_variant 4/63

Frequencies

GnomAD3 genomes
AF:
0.000670
AC:
102
AN:
152258
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000314
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00126
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000492
AC:
91
AN:
184846
Hom.:
0
AF XY:
0.000471
AC XY:
47
AN XY:
99728
show subpopulations
Gnomad AFR exome
AF:
0.000201
Gnomad AMR exome
AF:
0.0000356
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00111
Gnomad OTH exome
AF:
0.000206
GnomAD4 exome
AF:
0.000740
AC:
1055
AN:
1424746
Hom.:
0
Cov.:
31
AF XY:
0.000742
AC XY:
523
AN XY:
705256
show subpopulations
Gnomad4 AFR exome
AF:
0.000215
Gnomad4 AMR exome
AF:
0.0000254
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000406
Gnomad4 NFE exome
AF:
0.000933
Gnomad4 OTH exome
AF:
0.000406
GnomAD4 genome
AF:
0.000670
AC:
102
AN:
152258
Hom.:
0
Cov.:
34
AF XY:
0.000605
AC XY:
45
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.000314
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.00126
Gnomad4 OTH
AF:
0.000478
Alfa
AF:
0.00101
Hom.:
0
Bravo
AF:
0.000586

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024INTS1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
5.9
DANN
Benign
0.89
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs376165628; hg19: chr7-1510854; API