chr1-159065976-C-A

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

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.20
Variant links:
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
AIM2NM_004833.3 linkuse as main transcriptc.750G>T p.Pro250= synonymous_variant 4/6 ENST00000368130.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AIM2ENST00000368130.9 linkuse as main transcriptc.750G>T p.Pro250= synonymous_variant 4/61 NM_004833.3 P1

Frequencies

GnomAD3 genomes
AF:
0.00822
AC:
1245
AN:
151458
Hom.:
14
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0283
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00368
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000419
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.0000738
Gnomad OTH
AF:
0.00772
GnomAD3 exomes
AF:
0.00200
AC:
501
AN:
251052
Hom.:
13
AF XY:
0.00149
AC XY:
202
AN XY:
135710
show subpopulations
Gnomad AFR exome
AF:
0.0276
Gnomad AMR exome
AF:
0.00128
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000328
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000352
Gnomad OTH exome
AF:
0.000653
GnomAD4 exome
AF:
0.000814
AC:
1187
AN:
1458528
Hom.:
24
Cov.:
31
AF XY:
0.000678
AC XY:
492
AN XY:
725486
show subpopulations
Gnomad4 AFR exome
AF:
0.0304
Gnomad4 AMR exome
AF:
0.00133
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000351
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000153
Gnomad4 OTH exome
AF:
0.00138
GnomAD4 genome
AF:
0.00822
AC:
1246
AN:
151576
Hom.:
14
Cov.:
32
AF XY:
0.00780
AC XY:
578
AN XY:
74092
show subpopulations
Gnomad4 AFR
AF:
0.0282
Gnomad4 AMR
AF:
0.00368
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000419
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000738
Gnomad4 OTH
AF:
0.00764
Alfa
AF:
0.000411
Hom.:
0
Bravo
AF:
0.00943
Asia WGS
AF:
0.00173
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 08, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
0.12
DANN
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs34654901; hg19: chr1-159035766; API