chr10-44984028-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032023.4(RASSF4):c.288G>T(p.Glu96Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,598,326 control chromosomes in the GnomAD database, including 109 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 64 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 45 hom. )
Consequence
RASSF4
NM_032023.4 missense
NM_032023.4 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: -0.417
Genes affected
RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]
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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=0.0017531216).
BP6
?
Variant 10-44984028-G-T is Benign according to our data. Variant chr10-44984028-G-T is described in ClinVar as [Benign]. Clinvar id is 780862.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0149 (2272/152324) while in subpopulation AFR AF= 0.0499 (2076/41564). AF 95% confidence interval is 0.0482. There are 64 homozygotes in gnomad4. There are 1034 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 63 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASSF4 | NM_032023.4 | c.288G>T | p.Glu96Asp | missense_variant | 5/11 | ENST00000340258.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASSF4 | ENST00000340258.10 | c.288G>T | p.Glu96Asp | missense_variant | 5/11 | 1 | NM_032023.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2262AN: 152206Hom.: 63 Cov.: 33
GnomAD3 genomes
?
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2262
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GnomAD3 exomes AF: 0.00371 AC: 834AN: 224536Hom.: 15 AF XY: 0.00291 AC XY: 352AN XY: 120978
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GnomAD4 exome AF: 0.00174 AC: 2516AN: 1446002Hom.: 45 Cov.: 31 AF XY: 0.00159 AC XY: 1141AN XY: 717646
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GnomAD4 genome ? AF: 0.0149 AC: 2272AN: 152324Hom.: 64 Cov.: 33 AF XY: 0.0139 AC XY: 1034AN XY: 74486
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ESP6500AA
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217
ESP6500EA
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ExAC
?
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514
Asia WGS
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12
AN:
3478
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 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;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;.
MutationTaster
Benign
D;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Loss of helix (P = 0.0444);.;
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