19-40599249-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000308370.11(LTBP4):āc.199A>Cā(p.Ile67Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. I67I) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000308370.11 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LTBP4 | NM_001042544.1 | c.199A>C | p.Ile67Leu | missense_variant | 2/33 | NP_001036009.1 | ||
LTBP4 | NM_003573.2 | c.69A>C | p.Ala23= | synonymous_variant | 2/33 | NP_003564.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LTBP4 | ENST00000308370.11 | c.199A>C | p.Ile67Leu | missense_variant | 2/33 | 1 | ENSP00000311905 | A2 | ||
LTBP4 | ENST00000204005.13 | c.69A>C | p.Ala23= | synonymous_variant | 2/33 | 1 | ENSP00000204005 | A2 | ||
LTBP4 | ENST00000594537.2 | c.147A>C | p.Ala49= | synonymous_variant, NMD_transcript_variant | 2/6 | 5 | ENSP00000480629 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248212Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134708
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461390Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726948
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74334
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at