chr10-122572320-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001377530.1(DMBT1):c.194C>T(p.Pro65Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00205 in 1,613,176 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMBT1 | NM_001377530.1 | c.194C>T | p.Pro65Leu | missense_variant | 5/56 | ENST00000338354.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMBT1 | ENST00000338354.10 | c.194C>T | p.Pro65Leu | missense_variant | 5/56 | 1 | NM_001377530.1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00195 AC: 296AN: 152150Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00143 AC: 356AN: 249256Hom.: 0 AF XY: 0.00133 AC XY: 180AN XY: 135216
GnomAD4 exome AF: 0.00206 AC: 3010AN: 1460908Hom.: 5 Cov.: 31 AF XY: 0.00203 AC XY: 1473AN XY: 726746
GnomAD4 genome AF: 0.00194 AC: 296AN: 152268Hom.: 1 Cov.: 33 AF XY: 0.00201 AC XY: 150AN XY: 74472
ClinVar
Submissions by phenotype
DMBT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2022 | This variant is classified as likely 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