chr9-110136428-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007203.5(PALM2AKAP2):c.884G>A(p.Cys295Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00375 in 1,614,150 control chromosomes in the GnomAD database, including 173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 91 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 82 hom. )
Consequence
PALM2AKAP2
NM_007203.5 missense
NM_007203.5 missense
Scores
3
8
5
Clinical Significance
Conservation
PhyloP100: 5.23
Genes affected
PALM2AKAP2 (HGNC:33529): (PALM2 and AKAP2 fusion) This gene belongs to the paralemmin downstream gene (PDG) family defined in PMID:22855693. Paralemmin downstream genes may have evolved contiguously with the paralemmin genes and are associated with other paralemmin paralogs in humans and several other taxa. The gene encodes three distinct protein isoforms, the PALM2 isoform, the AKAP2 isoform and the PALM2-AKAP2 isoform. The biological significance of the PALM2-AKAP2 isoforms is yet unknown. Earlier, PALM2 and AKAP2 were annotated as separate genes and PALM2-AKAP2 was annotated as a readthrough gene. [provided by RefSeq, May 2019]
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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 (MetaRNN=0.0054033697).
BP6
?
Variant 9-110136428-G-A is Benign according to our data. Variant chr9-110136428-G-A is described in ClinVar as [Benign]. Clinvar id is 781172.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALM2AKAP2 | NM_007203.5 | c.884G>A | p.Cys295Tyr | missense_variant | 8/11 | ENST00000374530.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALM2AKAP2 | ENST00000374530.8 | c.884G>A | p.Cys295Tyr | missense_variant | 8/11 | 2 | NM_007203.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0186 AC: 2830AN: 152140Hom.: 91 Cov.: 32
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GnomAD3 exomes AF: 0.00506 AC: 1259AN: 249034Hom.: 36 AF XY: 0.00381 AC XY: 514AN XY: 134808
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GnomAD4 exome AF: 0.00221 AC: 3224AN: 1461892Hom.: 82 Cov.: 32 AF XY: 0.00193 AC XY: 1405AN XY: 727246
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GnomAD4 genome ? AF: 0.0186 AC: 2836AN: 152258Hom.: 91 Cov.: 32 AF XY: 0.0179 AC XY: 1332AN XY: 74426
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D;D
REVEL
Uncertain
Sift
Pathogenic
D;.;D;D;D;D
Sift4G
Benign
T;T;T;T;T;D
Polyphen
0.99, 0.99, 0.96
.;.;D;D;D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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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