10-99955525-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015221.4(DNMBP):c.1949C>T(p.Ser650Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,597,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNMBP | NM_015221.4 | c.1949C>T | p.Ser650Leu | missense_variant | 4/17 | ENST00000324109.9 | NP_056036.1 | |
DNMBP-AS1 | NR_024130.3 | n.177-149G>A | intron_variant, non_coding_transcript_variant | |||||
DNMBP | XM_011539559.3 | c.1949C>T | p.Ser650Leu | missense_variant | 5/18 | XP_011537861.1 | ||
DNMBP | XM_047424910.1 | c.1949C>T | p.Ser650Leu | missense_variant | 5/18 | XP_047280866.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNMBP | ENST00000324109.9 | c.1949C>T | p.Ser650Leu | missense_variant | 4/17 | 1 | NM_015221.4 | ENSP00000315659 | P1 | |
DNMBP-AS1 | ENST00000661385.1 | n.223-957G>A | intron_variant, non_coding_transcript_variant | |||||||
DNMBP-AS1 | ENST00000434409.2 | n.173-149G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
DNMBP-AS1 | ENST00000661150.1 | n.177-1264G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000419 AC: 1AN: 238606Hom.: 0 AF XY: 0.00000776 AC XY: 1AN XY: 128862
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1445678Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 717718
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2023 | The c.1949C>T (p.S650L) alteration is located in exon 4 (coding exon 3) of the DNMBP gene. This alteration results from a C to T substitution at nucleotide position 1949, causing the serine (S) at amino acid position 650 to be replaced by a leucine (L). 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