chr20-34075911-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_016732.3(RALY):c.415G>A(p.Val139Met) variant causes a missense change. The variant allele was found at a frequency of 0.0013 in 1,614,062 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.0070 ( 13 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 13 hom. )
Consequence
RALY
NM_016732.3 missense
NM_016732.3 missense
Scores
7
9
Clinical Significance
Conservation
PhyloP100: 6.01
Genes affected
RALY (HGNC:15921): (RALY heterogeneous nuclear ribonucleoprotein) This gene encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) gene family. This protein may play a role in pre-mRNA splicing and in embryonic development. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
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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=0.007173568).
BP6
?
Variant 20-34075911-G-A is Benign according to our data. Variant chr20-34075911-G-A is described in ClinVar as [Benign]. Clinvar id is 786970.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00697 (1061/152304) while in subpopulation AFR AF= 0.0236 (982/41572). AF 95% confidence interval is 0.0224. There are 13 homozygotes in gnomad4. There are 497 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RALY | NM_016732.3 | c.415G>A | p.Val139Met | missense_variant | 6/10 | ENST00000246194.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RALY | ENST00000246194.8 | c.415G>A | p.Val139Met | missense_variant | 6/10 | 1 | NM_016732.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00697 AC: 1060AN: 152186Hom.: 13 Cov.: 32
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GnomAD3 exomes AF: 0.00164 AC: 411AN: 250868Hom.: 1 AF XY: 0.00114 AC XY: 154AN XY: 135670
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GnomAD4 exome AF: 0.000705 AC: 1031AN: 1461758Hom.: 13 Cov.: 30 AF XY: 0.000606 AC XY: 441AN XY: 727180
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GnomAD4 genome ? AF: 0.00697 AC: 1061AN: 152304Hom.: 13 Cov.: 32 AF XY: 0.00667 AC XY: 497AN XY: 74462
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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 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
D;.;D;.;.
Vest4
MVP
MPC
1.4
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