10-99955546-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015221.4(DNMBP):c.1928G>A(p.Arg643His) variant causes a missense change. The variant allele was found at a frequency of 0.0000357 in 1,598,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R643C) has been classified as Uncertain significance.
Frequency
Consequence
NM_015221.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMBP | NM_015221.4 | c.1928G>A | p.Arg643His | missense_variant | Exon 4 of 17 | ENST00000324109.9 | NP_056036.1 | |
DNMBP | XM_011539559.3 | c.1928G>A | p.Arg643His | missense_variant | Exon 5 of 18 | XP_011537861.1 | ||
DNMBP | XM_047424910.1 | c.1928G>A | p.Arg643His | missense_variant | Exon 5 of 18 | XP_047280866.1 | ||
DNMBP-AS1 | NR_024130.3 | n.177-128C>T | intron_variant | Intron 2 of 4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.1928G>A | p.Arg643His | missense_variant | Exon 4 of 17 | 1 | NM_015221.4 | ENSP00000315659.4 | ||
DNMBP-AS1 | ENST00000434409.2 | n.173-128C>T | intron_variant | Intron 2 of 4 | 2 | |||||
DNMBP-AS1 | ENST00000661150.1 | n.177-1243C>T | intron_variant | Intron 2 of 2 | ||||||
DNMBP-AS1 | ENST00000661385.1 | n.223-936C>T | intron_variant | Intron 2 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 38AN: 238770Hom.: 0 AF XY: 0.000163 AC XY: 21AN XY: 129154
GnomAD4 exome AF: 0.0000304 AC: 44AN: 1446160Hom.: 0 Cov.: 31 AF XY: 0.0000292 AC XY: 21AN XY: 718136
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1928G>A (p.R643H) alteration is located in exon 4 (coding exon 3) of the DNMBP gene. This alteration results from a G to A substitution at nucleotide position 1928, causing the arginine (R) at amino acid position 643 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at