rs7383
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001377530.1(DMBT1):c.*193T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 765,614 control chromosomes in the GnomAD database, including 92,355 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 0.55 ( 25687 hom., cov: 32)
Exomes 𝑓: 0.45 ( 66668 hom. )
Consequence
DMBT1
NM_001377530.1 3_prime_UTR
NM_001377530.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.267
Genes affected
DMBT1 (HGNC:2926): (deleted in malignant brain tumors 1) Loss of sequences from human chromosome 10q has been associated with the progression of human cancers. This gene was originally isolated based on its deletion in a medulloblastoma cell line. This gene is expressed with transcripts of 6.0, 7.5, and 8.0 kb in fetal lung and with one transcript of 8.0 kb in adult lung, although the 7.5 kb transcript has not been characterized. The encoded protein precursor is a glycoprotein containing multiple scavenger receptor cysteine-rich (SRCR) domains separated by SRCR-interspersed domains (SID). Transcript variant 2 (8.0 kb) has been shown to bind surfactant protein D independently of carbohydrate recognition. This indicates that DMBT1 may not be a classical tumor suppressor gene, but rather play a role in the interaction of tumor cells and the immune system. [provided by RefSeq, Mar 2016]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMBT1 | NM_001377530.1 | c.*193T>C | 3_prime_UTR_variant | 56/56 | ENST00000338354.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMBT1 | ENST00000338354.10 | c.*193T>C | 3_prime_UTR_variant | 56/56 | 1 | NM_001377530.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.553 AC: 84022AN: 151864Hom.: 25644 Cov.: 32
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GnomAD4 exome AF: 0.449 AC: 275764AN: 613632Hom.: 66668 Cov.: 8 AF XY: 0.454 AC XY: 142481AN XY: 313628
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GnomAD4 genome ? AF: 0.554 AC: 84129AN: 151982Hom.: 25687 Cov.: 32 AF XY: 0.555 AC XY: 41227AN XY: 74268
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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