chr8-7416807-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001205266.2(DEFB4B):c.21C>T(p.Leu7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 0 hom., cov: 11)
Exomes 𝑓: 0.0027 ( 14 hom. )
Failed GnomAD Quality Control
Consequence
DEFB4B
NM_001205266.2 synonymous
NM_001205266.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.311
Genes affected
DEFB4B (HGNC:30193): (defensin beta 4B) Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Members of the defensin family are highly similar in protein sequence. This gene encodes defensin, beta 4, an antibiotic peptide which is locally regulated by inflammation. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 8-7416807-G-A is Benign according to our data. Variant chr8-7416807-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658362.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.311 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome at 5 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEFB4B | NM_001205266.2 | c.21C>T | p.Leu7= | synonymous_variant | 1/2 | ENST00000318157.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEFB4B | ENST00000318157.3 | c.21C>T | p.Leu7= | synonymous_variant | 1/2 | 1 | NM_001205266.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 283AN: 91636Hom.: 0 Cov.: 11 FAILED QC
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GnomAD3 exomes AF: 0.00183 AC: 215AN: 117440Hom.: 5 AF XY: 0.00163 AC XY: 101AN XY: 62018
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00268 AC: 2029AN: 756900Hom.: 14 Cov.: 13 AF XY: 0.00285 AC XY: 1094AN XY: 383984
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00307 AC: 282AN: 91726Hom.: 0 Cov.: 11 AF XY: 0.00299 AC XY: 128AN XY: 42866
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | DEFB4B: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at