chr7-78019216-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_012301.4(MAGI2):c.*99G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,375,632 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 24 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 21 hom. )
Consequence
MAGI2
NM_012301.4 3_prime_UTR
NM_012301.4 3_prime_UTR
Scores
4
Clinical Significance
Conservation
PhyloP100: 0.713
Genes affected
MAGI2 (HGNC:18957): (membrane associated guanylate kinase, WW and PDZ domain containing 2) The protein encoded by this gene interacts with atrophin-1. Atrophin-1 contains a polyglutamine repeat, expansion of which is responsible for dentatorubral and pallidoluysian atrophy. This encoded protein is characterized by two WW domains, a guanylate kinase-like domain, and multiple PDZ domains. It has structural similarity to the membrane-associated guanylate kinase homologue (MAGUK) family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 7-78019216-C-T is Benign according to our data. Variant chr7-78019216-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1317281.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0104 (1588/152262) while in subpopulation AFR AF= 0.036 (1495/41564). AF 95% confidence interval is 0.0345. There are 24 homozygotes in gnomad4. There are 758 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGI2 | NM_012301.4 | c.*99G>A | 3_prime_UTR_variant | 22/22 | ENST00000354212.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGI2 | ENST00000354212.9 | c.*99G>A | 3_prime_UTR_variant | 22/22 | 1 | NM_012301.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1588AN: 152144Hom.: 24 Cov.: 32
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GnomAD3 exomes AF: 0.00176 AC: 198AN: 112358Hom.: 1 AF XY: 0.00130 AC XY: 81AN XY: 62202
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GnomAD4 exome AF: 0.000946 AC: 1157AN: 1223370Hom.: 21 Cov.: 17 AF XY: 0.000799 AC XY: 488AN XY: 610546
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GnomAD4 genome ? AF: 0.0104 AC: 1588AN: 152262Hom.: 24 Cov.: 32 AF XY: 0.0102 AC XY: 758AN XY: 74462
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
D
MutationTaster
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D;D
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at