rs767424969
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001005361.3(DNM2):c.1782-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000054 in 1,609,786 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001005361.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNM2 | NM_001005361.3 | c.1782-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000389253.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNM2 | ENST00000389253.9 | c.1782-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001005361.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000528 AC: 8AN: 151600Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000640 AC: 16AN: 249898Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135494
GnomAD4 exome AF: 0.0000542 AC: 79AN: 1458186Hom.: 1 Cov.: 32 AF XY: 0.0000510 AC XY: 37AN XY: 725496
GnomAD4 genome AF: 0.0000528 AC: 8AN: 151600Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73972
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 04, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | DNM2: BP4 - |
Charcot-Marie-Tooth disease dominant intermediate B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at