rs35097575
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_017820.5(EXD3):c.1598C>T(p.Thr533Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 1,600,154 control chromosomes in the GnomAD database, including 2,088 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.037 ( 161 hom., cov: 32)
Exomes 𝑓: 0.049 ( 1927 hom. )
Consequence
EXD3
NM_017820.5 missense
NM_017820.5 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 1.96
Genes affected
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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=0.0020832121).
BP6
?
Variant 9-137349428-G-A is Benign according to our data. Variant chr9-137349428-G-A is described in ClinVar as [Benign]. Clinvar id is 402840.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EXD3 | NM_017820.5 | c.1598C>T | p.Thr533Met | missense_variant | 15/22 | ENST00000340951.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EXD3 | ENST00000340951.9 | c.1598C>T | p.Thr533Met | missense_variant | 15/22 | 1 | NM_017820.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0370 AC: 5625AN: 152178Hom.: 161 Cov.: 32
GnomAD3 genomes
?
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5625
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32
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GnomAD3 exomes AF: 0.0363 AC: 8331AN: 229656Hom.: 213 AF XY: 0.0380 AC XY: 4793AN XY: 126180
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GnomAD4 exome AF: 0.0489 AC: 70751AN: 1447858Hom.: 1927 Cov.: 35 AF XY: 0.0488 AC XY: 35157AN XY: 720032
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GnomAD4 genome ? AF: 0.0369 AC: 5624AN: 152296Hom.: 161 Cov.: 32 AF XY: 0.0372 AC XY: 2771AN XY: 74474
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ALSPAC
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190
ESP6500AA
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ExAC
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4282
Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
P
Vest4
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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