chr1-159068562-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004833.3(AIM2):c.396+6A>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00147 in 1,610,286 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0080 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00079 ( 21 hom. )
Consequence
AIM2
NM_004833.3 splice_donor_region, intron
NM_004833.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.00003995
2
Clinical Significance
Conservation
PhyloP100: -0.360
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 1-159068562-T-A is Benign according to our data. Variant chr1-159068562-T-A is described in ClinVar as [Benign]. Clinvar id is 780269.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00802 (1221/152320) while in subpopulation AFR AF= 0.0275 (1144/41564). AF 95% confidence interval is 0.0262. There are 11 homozygotes in gnomad4. There are 568 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AIM2 | NM_004833.3 | c.396+6A>T | splice_donor_region_variant, intron_variant | ENST00000368130.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AIM2 | ENST00000368130.9 | c.396+6A>T | splice_donor_region_variant, intron_variant | 1 | NM_004833.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00802 AC: 1220AN: 152202Hom.: 11 Cov.: 32
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GnomAD3 exomes AF: 0.00192 AC: 474AN: 247496Hom.: 12 AF XY: 0.00141 AC XY: 189AN XY: 133948
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GnomAD4 exome AF: 0.000789 AC: 1151AN: 1457966Hom.: 21 Cov.: 30 AF XY: 0.000666 AC XY: 483AN XY: 725296
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at