chr1-159065976-C-A
Position:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_004833.3(AIM2):c.750G>T(p.Pro250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 1,610,104 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0082 ( 14 hom., cov: 32)
Exomes 𝑓: 0.00081 ( 24 hom. )
Consequence
AIM2
NM_004833.3 synonymous
NM_004833.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.20
Genes affected
AIM2 (HGNC:357): (absent in melanoma 2) AIM2 is a member of the IFI20X /IFI16 family. It plays a putative role in tumorigenic reversion and may control cell proliferation. Interferon-gamma induces expression of AIM2. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 1-159065976-C-A is Benign according to our data. Variant chr1-159065976-C-A is described in ClinVar as [Benign]. Clinvar id is 780268.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.2 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00822 (1246/151576) while in subpopulation AFR AF= 0.0282 (1166/41334). AF 95% confidence interval is 0.0269. There are 14 homozygotes in gnomad4. There are 578 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIM2 | NM_004833.3 | c.750G>T | p.Pro250= | synonymous_variant | 4/6 | ENST00000368130.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIM2 | ENST00000368130.9 | c.750G>T | p.Pro250= | synonymous_variant | 4/6 | 1 | NM_004833.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00822 AC: 1245AN: 151458Hom.: 14 Cov.: 32
GnomAD3 genomes
AF:
AC:
1245
AN:
151458
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.00200 AC: 501AN: 251052Hom.: 13 AF XY: 0.00149 AC XY: 202AN XY: 135710
GnomAD3 exomes
AF:
AC:
501
AN:
251052
Hom.:
AF XY:
AC XY:
202
AN XY:
135710
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000814 AC: 1187AN: 1458528Hom.: 24 Cov.: 31 AF XY: 0.000678 AC XY: 492AN XY: 725486
GnomAD4 exome
AF:
AC:
1187
AN:
1458528
Hom.:
Cov.:
31
AF XY:
AC XY:
492
AN XY:
725486
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00822 AC: 1246AN: 151576Hom.: 14 Cov.: 32 AF XY: 0.00780 AC XY: 578AN XY: 74092
GnomAD4 genome
AF:
AC:
1246
AN:
151576
Hom.:
Cov.:
32
AF XY:
AC XY:
578
AN XY:
74092
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
6
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at