11-65546806-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001130144.3(LTBP3):āc.2222C>Gā(p.Ala741Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00699 in 1,604,476 control chromosomes in the GnomAD database, including 118 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001130144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP3 | NM_001130144.3 | c.2222C>G | p.Ala741Gly | missense_variant | 15/28 | ENST00000301873.11 | NP_001123616.1 | |
LTBP3 | NM_021070.4 | c.2222C>G | p.Ala741Gly | missense_variant | 15/27 | NP_066548.2 | ||
LTBP3 | NM_001164266.1 | c.1871C>G | p.Ala624Gly | missense_variant | 15/27 | NP_001157738.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0103 AC: 1568AN: 152174Hom.: 19 Cov.: 32
GnomAD3 exomes AF: 0.00790 AC: 1879AN: 237826Hom.: 15 AF XY: 0.00768 AC XY: 1002AN XY: 130458
GnomAD4 exome AF: 0.00665 AC: 9653AN: 1452188Hom.: 99 Cov.: 37 AF XY: 0.00678 AC XY: 4898AN XY: 722722
GnomAD4 genome AF: 0.0103 AC: 1563AN: 152288Hom.: 19 Cov.: 32 AF XY: 0.00965 AC XY: 719AN XY: 74472
ClinVar
Submissions by phenotype
Brachyolmia-amelogenesis imperfecta syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at