rs746506861
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001042545.2(LTBP4):c.211C>T(p.Pro71Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000334 in 1,407,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001042545.2 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 | UniProt |
---|---|---|---|---|---|---|---|
LTBP4 | NM_001042545.2 | c.211C>T | p.Pro71Ser | missense_variant | 1/30 | ENST00000396819.8 | |
LTBP4 | NM_001042544.1 | c.451+1421C>T | intron_variant | ||||
LTBP4 | NM_003573.2 | c.340+1421C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LTBP4 | ENST00000396819.8 | c.211C>T | p.Pro71Ser | missense_variant | 1/30 | 1 | NM_001042545.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152104Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000208 AC: 6AN: 28872Hom.: 0 AF XY: 0.000115 AC XY: 2AN XY: 17392
GnomAD4 exome AF: 0.0000335 AC: 42AN: 1255176Hom.: 0 Cov.: 31 AF XY: 0.0000293 AC XY: 18AN XY: 614170
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152104Hom.: 0 Cov.: 30 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Gene associated with AR cutis laxa - no clear association with PCD - should be removed from gene list. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at