7-156658494-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_030936.4(RNF32):ā€‹c.608G>Cā€‹(p.Arg203Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,490 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 (ā˜…).

Frequency

Genomes: š‘“ 0.000026 ( 0 hom., cov: 33)
Exomes š‘“: 0.000012 ( 0 hom. )

Consequence

RNF32
NM_030936.4 missense

Scores

8
9
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.29
Variant links:
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]
RNF32-AS1 (HGNC:40798): (RNF32 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.96

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RNF32NM_030936.4 linkuse as main transcriptc.608G>C p.Arg203Thr missense_variant 7/9 ENST00000317955.10 NP_112198.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RNF32ENST00000317955.10 linkuse as main transcriptc.608G>C p.Arg203Thr missense_variant 7/91 NM_030936.4 ENSP00000315950 P1Q9H0A6-1
RNF32-AS1ENST00000670834.1 linkuse as main transcriptn.1089C>G non_coding_transcript_exon_variant 1/3

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152146
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000116
AC:
17
AN:
1461344
Hom.:
0
Cov.:
30
AF XY:
0.0000151
AC XY:
11
AN XY:
727034
show subpopulations
Gnomad4 AFR exome
AF:
0.0000598
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000126
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152146
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000564
Hom.:
0
Bravo
AF:
0.0000189

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 submitterclinical testingAmbry GeneticsAug 08, 2022The c.608G>C (p.R203T) alteration is located in exon 7 (coding exon 6) of the RNF32 gene. This alteration results from a G to C substitution at nucleotide position 608, causing the arginine (R) at amino acid position 203 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.82
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.24
CADD
Uncertain
25
DANN
Uncertain
0.98
DEOGEN2
Benign
0.24
.;T;T;T;.;T;.
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.90
D;.;.;.;D;D;D
M_CAP
Uncertain
0.092
D
MetaRNN
Pathogenic
0.96
D;D;D;D;D;D;D
MetaSVM
Uncertain
0.12
D
MutationAssessor
Pathogenic
3.0
.;M;M;M;.;M;M
MutationTaster
Benign
1.0
D;D;D;D;D;D;D
PrimateAI
Uncertain
0.49
T
PROVEAN
Pathogenic
-5.6
D;D;D;D;D;D;D
REVEL
Pathogenic
0.72
Sift
Pathogenic
0.0
D;D;D;D;D;D;D
Sift4G
Uncertain
0.011
D;D;D;D;D;D;D
Polyphen
1.0
.;D;D;D;D;D;D
Vest4
0.61, 0.84, 0.84, 0.85, 0.82
MutPred
0.86
Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);Gain of glycosylation at R203 (P = 0.1143);
MVP
0.86
MPC
0.80
ClinPred
1.0
D
GERP RS
4.8
Varity_R
0.89
gMVP
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs970450561; hg19: chr7-156451188; API