7-156644740-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_030936.4(RNF32):c.257C>T(p.Pro86Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000028 in 1,608,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
RNF32
NM_030936.4 missense
NM_030936.4 missense
Scores
3
11
5
Clinical Significance
Conservation
PhyloP100: 5.15
Genes affected
RNF32 (HGNC:17118): (ring finger protein 32) The protein encoded by this gene contains two RING ring finger motifs. RING finger motifs are present in a variety of functionally distinct proteins and are known to be involved in protein-DNA or protein-protein interactions. This gene was found to be expressed during spermatogenesis, most likely in spermatocytes and/or in spermatids. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.801
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNF32 | NM_030936.4 | c.257C>T | p.Pro86Leu | missense_variant | 3/9 | ENST00000317955.10 | NP_112198.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNF32 | ENST00000317955.10 | c.257C>T | p.Pro86Leu | missense_variant | 3/9 | 1 | NM_030936.4 | ENSP00000315950 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243778Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131856
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GnomAD4 exome AF: 0.0000247 AC: 36AN: 1455890Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 723894
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GnomAD4 genome AF: 0.0000592 AC: 9AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74306
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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 | Dec 27, 2022 | The c.257C>T (p.P86L) alteration is located in exon 3 (coding exon 2) of the RNF32 gene. This alteration results from a C to T substitution at nucleotide position 257, causing the proline (P) at amino acid position 86 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;T;T;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;.;.;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
.;M;M;M;.;M;M
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
T;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D;D;D
Polyphen
1.0
.;D;D;D;D;D;D
Vest4
0.74, 0.72, 0.70, 0.71
MVP
MPC
0.66
ClinPred
D
GERP RS
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