chr4-37686239-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001085400.2(RELL1):c.49T>C(p.Phe17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00388 in 1,580,932 control chromosomes in the GnomAD database, including 212 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 119 hom., cov: 34)
Exomes 𝑓: 0.0020 ( 93 hom. )
Consequence
RELL1
NM_001085400.2 missense
NM_001085400.2 missense
Scores
1
4
12
Clinical Significance
Conservation
PhyloP100: 2.14
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0017594099).
BP6
?
Variant 4-37686239-A-G is Benign according to our data. Variant chr4-37686239-A-G is described in ClinVar as [Benign]. Clinvar id is 709677.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0738 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RELL1 | NM_001085400.2 | c.49T>C | p.Phe17Leu | missense_variant | 1/7 | ENST00000454158.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RELL1 | ENST00000454158.7 | c.49T>C | p.Phe17Leu | missense_variant | 1/7 | 5 | NM_001085400.2 | P1 | |
RELL1 | ENST00000314117.8 | c.49T>C | p.Phe17Leu | missense_variant | 1/7 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0216 AC: 3291AN: 152016Hom.: 119 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00378 AC: 747AN: 197384Hom.: 23 AF XY: 0.00293 AC XY: 325AN XY: 111074
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GnomAD4 exome AF: 0.00198 AC: 2835AN: 1428806Hom.: 93 Cov.: 31 AF XY: 0.00170 AC XY: 1207AN XY: 710844
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GnomAD4 genome ? AF: 0.0217 AC: 3300AN: 152126Hom.: 119 Cov.: 34 AF XY: 0.0209 AC XY: 1555AN XY: 74374
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ESP6500AA
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ExAC
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624
Asia WGS
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3470
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 | Apr 04, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
N;N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
T;T
Polyphen
B;B
Vest4
MutPred
Loss of catalytic residue at F17 (P = 0.0077);Loss of catalytic residue at F17 (P = 0.0077);
MVP
MPC
1.3
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