8-6936059-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001925.3(DEFA4):āc.255T>Cā(p.Gly85Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,613,472 control chromosomes in the GnomAD database, including 130,446 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.43 ( 14663 hom., cov: 33)
Exomes š: 0.39 ( 115783 hom. )
Consequence
DEFA4
NM_001925.3 synonymous
NM_001925.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.117
Genes affected
DEFA4 (HGNC:2763): (defensin alpha 4) Defensins are a family of antimicrobial and cytotoxic peptides thought to be involved in host defense. They are abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the intestine, respiratory tract, urinary tract, and vagina. Members of the defensin family are highly similar in protein sequence and distinguished by a conserved cysteine motif. Several alpha defensin genes are clustered on chromosome 8. This gene differs from other genes of this family by an extra 83-base segment that is apparently the result of a recent duplication within the coding region. The protein encoded by this gene, defensin, alpha 4, is found in the neutrophils; it exhibits corticostatic activity and inhibits corticotropin stimulated corticosterone production. [provided by RefSeq, Oct 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-0.117 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.427 AC: 64823AN: 151890Hom.: 14652 Cov.: 33
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GnomAD3 exomes AF: 0.389 AC: 97718AN: 251324Hom.: 20147 AF XY: 0.397 AC XY: 53867AN XY: 135852
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GnomAD4 exome AF: 0.392 AC: 573591AN: 1461466Hom.: 115783 Cov.: 46 AF XY: 0.395 AC XY: 286992AN XY: 727014
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GnomAD4 genome AF: 0.427 AC: 64880AN: 152006Hom.: 14663 Cov.: 33 AF XY: 0.424 AC XY: 31506AN XY: 74294
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at