6-3264247-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001128591.2(PSMG4):c.250+488G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,551,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
PSMG4
NM_001128591.2 intron
NM_001128591.2 intron
Scores
16
Clinical Significance
Conservation
PhyloP100: -3.98
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0054430068).
BP6
Variant 6-3264247-G-A is Benign according to our data. Variant chr6-3264247-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2356268.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMG4 | NM_001128591.2 | c.250+488G>A | intron_variant | ENST00000438998.7 | NP_001122063.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMG4 | ENST00000438998.7 | c.250+488G>A | intron_variant | 2 | NM_001128591.2 | ENSP00000413353 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152224Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000344 AC: 53AN: 154102Hom.: 0 AF XY: 0.000355 AC XY: 29AN XY: 81740
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GnomAD4 exome AF: 0.000126 AC: 176AN: 1399134Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 93AN XY: 690094
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GnomAD4 genome AF: 0.000203 AC: 31AN: 152342Hom.: 0 Cov.: 34 AF XY: 0.000228 AC XY: 17AN XY: 74488
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
ClinPred
T
GERP RS
gMVP
Splicing
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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