chr15-56094316-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_022841.7(RFX7):c.3412A>T(p.Asn1138Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00306 in 1,613,942 control chromosomes in the GnomAD database, including 150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0049 ( 22 hom., cov: 32)
Exomes 𝑓: 0.0029 ( 128 hom. )
Consequence
RFX7
NM_022841.7 missense
NM_022841.7 missense
Scores
1
6
10
Clinical Significance
Conservation
PhyloP100: 4.65
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=0.003949195).
BP6
?
Variant 15-56094316-T-A is Benign according to our data. Variant chr15-56094316-T-A is described in ClinVar as [Benign]. Clinvar id is 789075.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0557 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFX7 | NM_022841.7 | c.3412A>T | p.Asn1138Tyr | missense_variant | 10/10 | ENST00000559447.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFX7 | ENST00000559447.8 | c.3412A>T | p.Asn1138Tyr | missense_variant | 10/10 | 5 | NM_022841.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00486 AC: 740AN: 152136Hom.: 23 Cov.: 32
GnomAD3 genomes
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740
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152136
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32
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GnomAD3 exomes AF: 0.0103 AC: 2576AN: 249038Hom.: 83 AF XY: 0.00788 AC XY: 1065AN XY: 135100
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GnomAD4 exome AF: 0.00288 AC: 4204AN: 1461688Hom.: 128 Cov.: 33 AF XY: 0.00253 AC XY: 1842AN XY: 727128
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GnomAD4 genome ? AF: 0.00486 AC: 740AN: 152254Hom.: 22 Cov.: 32 AF XY: 0.00504 AC XY: 375AN XY: 74438
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740
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ESP6500AA
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ExAC
?
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1034
Asia WGS
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3478
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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 | Apr 09, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
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