rs1799946
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005218.4(DEFB1):c.-52G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,557,256 control chromosomes in the GnomAD database, including 106,304 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: 𝑓 0.41 ( 13422 hom., cov: 32)
Exomes 𝑓: 0.36 ( 92882 hom. )
Consequence
DEFB1
NM_005218.4 5_prime_UTR
NM_005218.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.49
Genes affected
DEFB1 (HGNC:2766): (defensin beta 1) 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 1, an antimicrobial peptide implicated in the resistance of epithelial surfaces to microbial colonization. This gene maps in close proximity to defensin family member, defensin, alpha 1 and has been implicated in the pathogenesis of cystic fibrosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEFB1 | NM_005218.4 | c.-52G>A | 5_prime_UTR_variant | 1/2 | ENST00000297439.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEFB1 | ENST00000297439.4 | c.-52G>A | 5_prime_UTR_variant | 1/2 | 1 | NM_005218.4 | P1 | ||
GS1-24F4.2 | ENST00000531701.1 | n.226-7213C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.405 AC: 61510AN: 151926Hom.: 13381 Cov.: 32
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GnomAD3 exomes AF: 0.362 AC: 89998AN: 248942Hom.: 17421 AF XY: 0.363 AC XY: 48918AN XY: 134632
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GnomAD4 exome AF: 0.359 AC: 505046AN: 1405212Hom.: 92882 Cov.: 21 AF XY: 0.360 AC XY: 253159AN XY: 702270
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GnomAD4 genome ? AF: 0.405 AC: 61603AN: 152044Hom.: 13422 Cov.: 32 AF XY: 0.400 AC XY: 29693AN XY: 74318
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ClinVar
Not reported inComputational scores
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Name
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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