rs539110133
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001130144.3(LTBP3):c.*8_*16delGACGCCGCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000551 in 1,364,696 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001130144.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.*8_*16delGACGCCGCC | 3_prime_UTR_variant | Exon 28 of 28 | ENST00000301873.11 | NP_001123616.1 | ||
LTBP3 | NM_021070.4 | c.*8_*16delGACGCCGCC | 3_prime_UTR_variant | Exon 27 of 27 | NP_066548.2 | |||
LTBP3 | NM_001164266.1 | c.*8_*16delGACGCCGCC | 3_prime_UTR_variant | Exon 27 of 27 | NP_001157738.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000461 AC: 70AN: 152008Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000742 AC: 27AN: 36384Hom.: 2 AF XY: 0.000604 AC XY: 13AN XY: 21538
GnomAD4 exome AF: 0.000562 AC: 682AN: 1212688Hom.: 4 AF XY: 0.000517 AC XY: 305AN XY: 589414
GnomAD4 genome AF: 0.000461 AC: 70AN: 152008Hom.: 1 Cov.: 33 AF XY: 0.000323 AC XY: 24AN XY: 74262
ClinVar
Submissions by phenotype
LTBP3-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