22-19524420-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP4_StrongBS2
The NM_003277.4(CLDN5):c.91G>A(p.Gly31Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000038 in 1,446,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003277.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLDN5 | NM_001130861.1 | c.91G>A | p.Gly31Ser | missense_variant | Exon 1 of 1 | NP_001124333.1 | ||
CLDN5 | NM_001363067.2 | c.91G>A | p.Gly31Ser | missense_variant | Exon 2 of 2 | NP_001349996.1 | ||
CLDN5 | NM_003277.4 | c.91G>A | p.Gly31Ser | missense_variant | Exon 2 of 2 | NP_003268.2 | ||
CLDN5 | NM_001363066.2 | c.-165G>A | upstream_gene_variant | ENST00000618236.2 | NP_001349995.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLDN5 | ENST00000403084.1 | c.91G>A | p.Gly31Ser | missense_variant | Exon 1 of 1 | 6 | ENSP00000384554.1 | |||
CLDN5 | ENST00000406028.1 | c.91G>A | p.Gly31Ser | missense_variant | Exon 2 of 2 | 2 | ENSP00000385477.1 | |||
CLDN5 | ENST00000413119.2 | c.91G>A | p.Gly31Ser | missense_variant | Exon 2 of 2 | 2 | ENSP00000400612.2 | |||
CLDN5 | ENST00000618236.2 | c.-165G>A | upstream_gene_variant | 6 | NM_001363066.2 | ENSP00000480623.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000646 AC: 4AN: 61892Hom.: 0 AF XY: 0.0000960 AC XY: 3AN XY: 31248
GnomAD4 exome AF: 0.0000371 AC: 48AN: 1294334Hom.: 0 Cov.: 34 AF XY: 0.0000446 AC XY: 28AN XY: 628172
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at