X-108440158-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_033380.3(COL4A5):c.33C>T(p.Gly11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,205,591 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 47 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000083 ( 0 hom., 3 hem., cov: 20)
Exomes 𝑓: 0.00013 ( 0 hom. 44 hem. )
Consequence
COL4A5
NM_033380.3 synonymous
NM_033380.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.31
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=-0.33).
BP6
Variant X-108440158-C-T is Benign according to our data. Variant chrX-108440158-C-T is described in ClinVar as [Benign]. Clinvar id is 1967561.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.32 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.33C>T | p.Gly11= | synonymous_variant | 1/53 | ENST00000328300.11 | NP_203699.1 | |
COL4A5 | NM_000495.5 | c.33C>T | p.Gly11= | synonymous_variant | 1/51 | NP_000486.1 | ||
COL4A5 | XM_047441811.1 | c.33C>T | p.Gly11= | synonymous_variant | 1/42 | XP_047297767.1 | ||
COL4A5 | XM_047441810.1 | c.-344C>T | 5_prime_UTR_variant | 1/54 | XP_047297766.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.33C>T | p.Gly11= | synonymous_variant | 1/53 | 1 | NM_033380.3 | ENSP00000331902 |
Frequencies
GnomAD3 genomes AF: 0.0000826 AC: 9AN: 108931Hom.: 0 Cov.: 20 AF XY: 0.0000962 AC XY: 3AN XY: 31197
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GnomAD3 exomes AF: 0.0000772 AC: 14AN: 181428Hom.: 0 AF XY: 0.0000604 AC XY: 4AN XY: 66176
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GnomAD4 exome AF: 0.000129 AC: 142AN: 1096660Hom.: 0 Cov.: 29 AF XY: 0.000122 AC XY: 44AN XY: 362070
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GnomAD4 genome AF: 0.0000826 AC: 9AN: 108931Hom.: 0 Cov.: 20 AF XY: 0.0000962 AC XY: 3AN XY: 31197
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Oct 07, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at