chr10-99877205-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015221.4(DNMBP):c.4680C>A(p.Asn1560Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000985 in 1,613,742 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_015221.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMBP | NM_015221.4 | c.4680C>A | p.Asn1560Lys | missense_variant | 17/17 | ENST00000324109.9 | NP_056036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.4680C>A | p.Asn1560Lys | missense_variant | 17/17 | 1 | NM_015221.4 | ENSP00000315659 | P1 | |
DNMBP | ENST00000543621.6 | c.2544C>A | p.Asn848Lys | missense_variant | 14/14 | 1 | ENSP00000443657 | |||
DNMBP | ENST00000636706.1 | c.3576C>A | p.Asn1192Lys | missense_variant | 14/14 | 2 | ENSP00000489875 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000877 AC: 22AN: 250964Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135636
GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461622Hom.: 1 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727086
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 30, 2024 | The c.4680C>A (p.N1560K) alteration is located in exon 17 (coding exon 16) of the DNMBP gene. This alteration results from a C to A substitution at nucleotide position 4680, causing the asparagine (N) at amino acid position 1560 to be replaced by a lysine (K). 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