rs104886047
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_033380.3(COL4A5):āc.90T>Cā(p.Tyr30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,207,069 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0000090 ( 0 hom., 0 hem., cov: 23)
Exomes š: 0.000016 ( 0 hom. 5 hem. )
Consequence
COL4A5
NM_033380.3 synonymous
NM_033380.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.04
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant X-108539754-T-C is Benign according to our data. Variant chrX-108539754-T-C is described in ClinVar as [Benign]. Clinvar id is 1169616.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
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Synonymous conserved (PhyloP=1.04 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome4 at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.90T>C | p.Tyr30= | synonymous_variant | 2/53 | ENST00000328300.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.90T>C | p.Tyr30= | synonymous_variant | 2/53 | 1 | NM_033380.3 | ||
COL4A5 | ENST00000361603.7 | c.90T>C | p.Tyr30= | synonymous_variant | 2/51 | 2 | P1 | ||
COL4A5 | ENST00000470339.1 | n.274T>C | non_coding_transcript_exon_variant | 2/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111653Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33823
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GnomAD3 exomes AF: 0.0000492 AC: 9AN: 182906Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67542
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GnomAD4 exome AF: 0.0000155 AC: 17AN: 1095416Hom.: 0 Cov.: 28 AF XY: 0.0000139 AC XY: 5AN XY: 360950
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GnomAD4 genome ? AF: 0.00000896 AC: 1AN: 111653Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33823
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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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