rs2680507
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_080389.3(DEFB104A):āc.28A>Gā(p.Ile10Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: š 0.33 ( 1782 hom., cov: 35)
Exomes š: 0.39 ( 13779 hom. )
Failed GnomAD Quality Control
Consequence
DEFB104A
NM_080389.3 missense
NM_080389.3 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.367
Genes affected
DEFB104A (HGNC:18115): (defensin beta 104A) Defensins form a family of antimicrobial and cytotoxic peptides made by neutrophils. Defensins are short, processed peptide molecules that are classified by structure into three groups: alpha-defensins, beta-defensins and theta-defensins. All beta-defensin genes are densely clustered in four to five syntenic chromosomal regions. Chromosome 8p23 contains at least two copies of the duplicated beta-defensin cluster. This duplication results in two identical copies of defensin, beta 104, DEFB104A and DEFB104B, in head-to-head orientation. This gene, DEFB104A, represents the more centromeric copy. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0021951199).
BP6
?
Variant 8-7836512-A-G is Benign according to our data. Variant chr8-7836512-A-G is described in ClinVar as [Benign]. Clinvar id is 768224.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEFB104A | NM_080389.3 | c.28A>G | p.Ile10Val | missense_variant | 1/2 | ENST00000314265.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEFB104A | ENST00000314265.3 | c.28A>G | p.Ile10Val | missense_variant | 1/2 | 1 | NM_080389.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 45048AN: 136172Hom.: 1784 Cov.: 35 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.388 AC: 472263AN: 1215682Hom.: 13779 Cov.: 30 AF XY: 0.388 AC XY: 234134AN XY: 604156
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.331 AC: 45059AN: 136264Hom.: 1782 Cov.: 35 AF XY: 0.332 AC XY: 22082AN XY: 66434
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Data not reliable, filtered out with message: InbreedingCoeff
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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 | Jun 26, 2017 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MPC
ClinPred
T
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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