chrX-108665559-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_033380.3(COL4A5):c.3426C>T(p.Pro1142=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000034 in 1,205,729 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1142P) has been classified as Likely benign.
Frequency
Consequence
NM_033380.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.3426C>T | p.Pro1142= | synonymous_variant | 38/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.3426C>T | p.Pro1142= | synonymous_variant | 38/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000361603.7 | c.3426C>T | p.Pro1142= | synonymous_variant | 38/51 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000196 AC: 22AN: 111961Hom.: 0 Cov.: 23 AF XY: 0.000205 AC XY: 7AN XY: 34127
GnomAD3 exomes AF: 0.0000278 AC: 5AN: 179941Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 64899
GnomAD4 exome AF: 0.0000174 AC: 19AN: 1093715Hom.: 0 Cov.: 28 AF XY: 0.0000111 AC XY: 4AN XY: 359399
GnomAD4 genome AF: 0.000196 AC: 22AN: 112014Hom.: 0 Cov.: 23 AF XY: 0.000205 AC XY: 7AN XY: 34190
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at