19-2430889-TGTGTGGATGAGGA-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_032737.4(LMNB2):c.*9_*21delTCCTCATCCACAC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000519 in 1,484,524 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_032737.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNB2 | ENST00000325327 | c.*9_*21delTCCTCATCCACAC | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_032737.4 | ENSP00000327054.3 | |||
LMNB2 | ENST00000475819.1 | n.48-594_48-582delTCCTCATCCACAC | intron_variant | Intron 1 of 1 | 5 | |||||
LMNB2 | ENST00000532465.1 | n.413+646_413+658delTCCTCATCCACAC | intron_variant | Intron 4 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152062Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251146Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135852
GnomAD4 exome AF: 0.0000540 AC: 72AN: 1332344Hom.: 1 AF XY: 0.0000746 AC XY: 50AN XY: 670128
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74402
ClinVar
Submissions by phenotype
LMNB2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at