chr10-99879859-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_015221.4(DNMBP):c.4500G>A(p.Pro1500Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00472 in 1,614,234 control chromosomes in the GnomAD database, including 195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_015221.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.4500G>A | p.Pro1500Pro | synonymous_variant | Exon 16 of 17 | 1 | NM_015221.4 | ENSP00000315659.4 | ||
DNMBP | ENST00000543621.6 | c.2364G>A | p.Pro788Pro | synonymous_variant | Exon 13 of 14 | 1 | ENSP00000443657.2 | |||
DNMBP | ENST00000636706.1 | c.3396G>A | p.Pro1132Pro | synonymous_variant | Exon 13 of 14 | 2 | ENSP00000489875.1 |
Frequencies
GnomAD3 genomes AF: 0.00534 AC: 813AN: 152222Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.0116 AC: 2907AN: 251072Hom.: 90 AF XY: 0.00998 AC XY: 1354AN XY: 135730
GnomAD4 exome AF: 0.00465 AC: 6802AN: 1461894Hom.: 172 Cov.: 31 AF XY: 0.00447 AC XY: 3251AN XY: 727248
GnomAD4 genome AF: 0.00532 AC: 810AN: 152340Hom.: 23 Cov.: 32 AF XY: 0.00593 AC XY: 442AN XY: 74486
ClinVar
Submissions by phenotype
DNMBP-related disorder Benign:1
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