7-1470934-G-A

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

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.420
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 -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
INTS1NM_001080453.3 linkuse as main transcriptc.6369C>T p.Pro2123= synonymous_variant 47/48 ENST00000404767.8
INTS1XM_011515260.2 linkuse as main transcriptc.6399C>T p.Pro2133= synonymous_variant 47/48

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
INTS1ENST00000404767.8 linkuse as main transcriptc.6369C>T p.Pro2123= synonymous_variant 47/485 NM_001080453.3 P1
INTS1ENST00000493446.1 linkuse as main transcriptn.353C>T non_coding_transcript_exon_variant 5/63

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000109
AC:
2
AN:
183566
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
99030
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000772
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000559
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000703
AC:
10
AN:
1422124
Hom.:
0
Cov.:
31
AF XY:
0.00000426
AC XY:
3
AN XY:
703936
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000538
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000607
Gnomad4 NFE exome
AF:
0.00000366
Gnomad4 OTH exome
AF:
0.0000169
GnomAD4 genome
Cov.:
33
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

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 providedclinical testingPreventionGenetics, part of Exact SciencesJun 18, 2019This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
CADD
Benign
9.5
DANN
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs757898200; hg19: chr7-1510570; API