chr10-122570905-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001377530.1(DMBT1):c.155C>G(p.Ser52Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.015 in 1,613,340 control chromosomes in the GnomAD database, including 1,509 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001377530.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMBT1 | NM_001377530.1 | c.155C>G | p.Ser52Trp | missense_variant | 4/56 | ENST00000338354.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMBT1 | ENST00000338354.10 | c.155C>G | p.Ser52Trp | missense_variant | 4/56 | 1 | NM_001377530.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0572 AC: 8701AN: 152116Hom.: 771 Cov.: 33
GnomAD3 exomes AF: 0.0172 AC: 4290AN: 249214Hom.: 314 AF XY: 0.0140 AC XY: 1893AN XY: 135198
GnomAD4 exome AF: 0.0106 AC: 15555AN: 1461106Hom.: 733 Cov.: 31 AF XY: 0.00983 AC XY: 7148AN XY: 726904
GnomAD4 genome ? AF: 0.0573 AC: 8717AN: 152234Hom.: 776 Cov.: 33 AF XY: 0.0559 AC XY: 4159AN XY: 74438
ClinVar
Submissions by phenotype
DMBT1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 05, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at