chr13-24793250-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_031277.3(RNF17):c.1144G>A(p.Val382Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00192 in 1,614,028 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 27 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 23 hom. )
Consequence
RNF17
NM_031277.3 missense
NM_031277.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 0.701
Genes affected
RNF17 (HGNC:10060): (ring finger protein 17) This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]
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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=0.002454251).
BP6
?
Variant 13-24793250-G-A is Benign according to our data. Variant chr13-24793250-G-A is described in ClinVar as [Benign]. Clinvar id is 784268.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0101 (1538/152266) while in subpopulation AFR AF= 0.0355 (1473/41550). AF 95% confidence interval is 0.0339. There are 27 homozygotes in gnomad4. There are 723 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 27 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF17 | NM_031277.3 | c.1144G>A | p.Val382Ile | missense_variant | 10/36 | ENST00000255324.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF17 | ENST00000255324.10 | c.1144G>A | p.Val382Ile | missense_variant | 10/36 | 2 | NM_031277.3 | P1 | |
RNF17 | ENST00000255325.6 | c.1144G>A | p.Val382Ile | missense_variant | 10/15 | 2 | |||
RNF17 | ENST00000255326.4 | n.1147G>A | non_coding_transcript_exon_variant | 10/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1540AN: 152148Hom.: 27 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00272 AC: 680AN: 250438Hom.: 13 AF XY: 0.00178 AC XY: 241AN XY: 135318
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GnomAD4 exome AF: 0.00107 AC: 1559AN: 1461762Hom.: 23 Cov.: 32 AF XY: 0.000865 AC XY: 629AN XY: 727182
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GnomAD4 genome ? AF: 0.0101 AC: 1538AN: 152266Hom.: 27 Cov.: 33 AF XY: 0.00971 AC XY: 723AN XY: 74454
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ESP6500AA
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167
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?
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403
Asia WGS
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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 | May 14, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
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