chr12-49642274-A-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001031698.3(PRPF40B):āc.1924A>Gā(p.Lys642Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,613,992 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00019 ( 0 hom., cov: 32)
Exomes š: 0.00016 ( 1 hom. )
Consequence
PRPF40B
NM_001031698.3 missense
NM_001031698.3 missense
Scores
2
7
10
Clinical Significance
Conservation
PhyloP100: 8.68
Genes affected
PRPF40B (HGNC:25031): (pre-mRNA processing factor 40 homolog B) This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to interact with Huntingtin and methyl CpG binding protein 2 (MeCP2). Alternative splicing results in different transcript variants. [provided by RefSeq, Aug 2014]
FMNL3 (HGNC:23698): (formin like 3) The protein encoded by this gene contains a formin homology 2 domain and has high sequence identity to the mouse Wbp3 protein. Two alternative transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.07775915).
BS2
High AC in GnomAd4 at 29 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF40B | NM_001031698.3 | c.1924A>G | p.Lys642Glu | missense_variant | 20/26 | ENST00000548825.7 | NP_001026868.2 | |
FMNL3 | NM_175736.5 | c.*3541T>C | 3_prime_UTR_variant | 26/26 | ENST00000335154.10 | NP_783863.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF40B | ENST00000548825.7 | c.1924A>G | p.Lys642Glu | missense_variant | 20/26 | 5 | NM_001031698.3 | ENSP00000448073 | P3 | |
FMNL3 | ENST00000335154.10 | c.*3541T>C | 3_prime_UTR_variant | 26/26 | 1 | NM_175736.5 | ENSP00000335655 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152076Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000264 AC: 66AN: 249796Hom.: 0 AF XY: 0.000281 AC XY: 38AN XY: 135138
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GnomAD4 exome AF: 0.000157 AC: 229AN: 1461798Hom.: 1 Cov.: 31 AF XY: 0.000177 AC XY: 129AN XY: 727208
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GnomAD4 genome AF: 0.000191 AC: 29AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74422
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2024 | The c.1858A>G (p.K620E) alteration is located in exon 19 (coding exon 19) of the PRPF40B gene. This alteration results from a A to G substitution at nucleotide position 1858, causing the lysine (K) at amino acid position 620 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
.;D;D
REVEL
Uncertain
Sift
Uncertain
.;D;D
Sift4G
Benign
T;T;T
Polyphen
1.0, 0.76
.;D;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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