rs374648340
Positions:
- chr12-26937997-G-GCACACACACA
- chr12-26937997-G-GCACACACACACACACACACACACACA
- chr12-26937997-G-GCACACACACACACACACACACACA
- chr12-26937997-G-GCACACACACACACACACACACA
- chr12-26937997-G-GCACACACACACACACACACA
- chr12-26937997-G-GCACACACACACACACA
- chr12-26937997-G-GCACACACACACACACACA
- chr12-26937997-GCA-G
- chr12-26937997-G-GCACACACA
- chr12-26937997-G-GCACACACACACA
- chr12-26937997-G-GCACACACACACACA
- chr12-26937997-G-GCACACA
- chr12-26937997-G-GCA
- chr12-26937997-G-GCACA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000544548.5(INTS13):c.-163-189_-163-188insTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00224 in 150,732 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0022 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
INTS13
ENST00000544548.5 intron
ENST00000544548.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.339
Genes affected
INTS13 (HGNC:20174): (integrator complex subunit 13) Involved in regulation of mitotic cell cycle. Acts upstream of or within centrosome localization; mitotic spindle organization; and protein localization to nuclear envelope. Located in cytoplasm and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| INTS13 | NM_018164.3 | upstream_gene_variant | ENST00000261191.12 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| INTS13 | ENST00000537336.1 | c.-12+270_-12+271insTGTGTGTGTG | intron_variant | 3 | |||||
| INTS13 | ENST00000544548.5 | c.-163-189_-163-188insTGTGTGTGTG | intron_variant | 3 | |||||
| INTS13 | ENST00000261191.12 | upstream_gene_variant | 1 | NM_018164.3 | P1 | ||||
| INTS13 | ENST00000538727.5 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes 0.00224 AC: 338AN: 150618Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
338
AN:
150618
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 570Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 370
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
570
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
370
Gnomad4 AFR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome 0.00224 AC: 338AN: 150732Hom.: 0 Cov.: 30 AF XY: 0.00206 AC XY: 152AN XY: 73688
GnomAD4 genome
AF:
AC:
338
AN:
150732
Hom.:
Cov.:
30
AF XY:
AC XY:
152
AN XY:
73688
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at