chrX-108449075-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_033380.3(COL4A5):c.81+8869C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.75 ( 22583 hom., 24329 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
COL4A5
NM_033380.3 intron
NM_033380.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.582
Genes affected
COL4A5 (HGNC:2207): (collagen type IV alpha 5 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Mutations in this gene are associated with X-linked Alport syndrome, also known as hereditary nephritis. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. Alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant X-108449075-C-T is Benign according to our data. Variant chrX-108449075-C-T is described in Lovd as [Benign].
BS2
?
High Homozygotes in GnomAd at 22586 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.81+8869C>T | intron_variant | ENST00000328300.11 | |||
COL4A5 | NM_000495.5 | c.81+8869C>T | intron_variant | ||||
COL4A5 | XM_047441810.1 | c.-296+8869C>T | intron_variant | ||||
COL4A5 | XM_047441811.1 | c.81+8869C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.81+8869C>T | intron_variant | 1 | NM_033380.3 | ||||
COL4A5 | ENST00000361603.7 | c.81+8869C>T | intron_variant | 2 | P1 | ||||
COL4A5 | ENST00000642185.1 | c.*122+8571C>T | intron_variant, NMD_transcript_variant | ||||||
COL4A5 | ENST00000470339.1 | n.265+8869C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.752 AC: 82985AN: 110316Hom.: 22586 Cov.: 23 AF XY: 0.746 AC XY: 24292AN XY: 32562
GnomAD3 genomes
?
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.752 AC: 83011AN: 110366Hom.: 22583 Cov.: 23 AF XY: 0.746 AC XY: 24329AN XY: 32622
GnomAD4 genome
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at