19-2456663-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_032737.4(LMNB2):c.264+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000422 in 1,517,716 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_032737.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LMNB2 | NM_032737.4 | c.264+7G>T | splice_region_variant, intron_variant | ENST00000325327.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327.4 | c.264+7G>T | splice_region_variant, intron_variant | 1 | NM_032737.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151764Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000249 AC: 4AN: 160528Hom.: 0 AF XY: 0.0000331 AC XY: 3AN XY: 90598
GnomAD4 exome AF: 0.0000417 AC: 57AN: 1365952Hom.: 0 Cov.: 31 AF XY: 0.0000443 AC XY: 30AN XY: 677798
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151764Hom.: 0 Cov.: 30 AF XY: 0.0000540 AC XY: 4AN XY: 74116
ClinVar
Submissions by phenotype
Lipodystrophy, partial, acquired, susceptibility to;C4225289:Progressive myoclonic epilepsy type 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at