chr10-122560784-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001377530.1(DMBT1):c.14C>A(p.Thr5Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,573,456 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_001377530.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMBT1 | NM_001377530.1 | c.14C>A | p.Thr5Lys | missense_variant | 1/56 | ENST00000338354.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMBT1 | ENST00000338354.10 | c.14C>A | p.Thr5Lys | missense_variant | 1/56 | 1 | NM_001377530.1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000591 AC: 90AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000166 AC: 32AN: 192378Hom.: 0 AF XY: 0.0000880 AC XY: 9AN XY: 102250
GnomAD4 exome AF: 0.0000570 AC: 81AN: 1421122Hom.: 0 Cov.: 30 AF XY: 0.0000555 AC XY: 39AN XY: 702820
GnomAD4 genome ? AF: 0.000591 AC: 90AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.000497 AC XY: 37AN XY: 74486
ClinVar
Submissions by phenotype
DMBT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2023 | 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