rs104886192
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP4_StrongBS2
The ENST00000328300.11(COL4A5):āc.2692A>Gā(p.Met898Val) variant causes a missense change. The variant allele was found at a frequency of 0.000221 in 1,203,910 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 85 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.00020 ( 0 hom., 8 hem., cov: 23)
Exomes š: 0.00022 ( 0 hom. 77 hem. )
Consequence
COL4A5
ENST00000328300.11 missense
ENST00000328300.11 missense
Scores
5
12
Clinical Significance
Conservation
PhyloP100: 5.54
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 Likely_benign. Variant got -6 ACMG points.
PM1
In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 0 uncertain in ENST00000328300.11
BP4
Computational evidence support a benign effect (MetaRNN=0.053881973).
BS2
High Hemizygotes in GnomAd4 at 8 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL4A5 | NM_033380.3 | c.2692A>G | p.Met898Val | missense_variant | 32/53 | ENST00000328300.11 | NP_203699.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL4A5 | ENST00000328300.11 | c.2692A>G | p.Met898Val | missense_variant | 32/53 | 1 | NM_033380.3 | ENSP00000331902 | ||
COL4A5 | ENST00000483338.1 | c.1516A>G | p.Met506Val | missense_variant | 16/20 | 1 | ENSP00000495685 | |||
COL4A5 | ENST00000361603.7 | c.2692A>G | p.Met898Val | missense_variant | 32/51 | 2 | ENSP00000354505 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000196 AC: 22AN: 112245Hom.: 0 Cov.: 23 AF XY: 0.000233 AC XY: 8AN XY: 34395
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GnomAD3 exomes AF: 0.000304 AC: 55AN: 181177Hom.: 0 AF XY: 0.000425 AC XY: 28AN XY: 65893
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GnomAD4 exome AF: 0.000224 AC: 244AN: 1091665Hom.: 0 Cov.: 28 AF XY: 0.000215 AC XY: 77AN XY: 357385
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GnomAD4 genome AF: 0.000196 AC: 22AN: 112245Hom.: 0 Cov.: 23 AF XY: 0.000233 AC XY: 8AN XY: 34395
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:3Uncertain:1Benign:7
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
X-linked Alport syndrome Pathogenic:2Uncertain:1Benign:2
Uncertain significance, flagged submission | clinical testing | Genome-Nilou Lab | May 18, 2021 | - - |
Pathogenic, criteria provided, single submitter | research | Laboratory of Prof. Karen Avraham, Tel Aviv University | May 01, 2024 | Pathogenic by Deafness Variation Database based on PMID:30773290 - |
Pathogenic, flagged submission | clinical testing | Medical Genetics, University of Parma | Mar 11, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | Aug 30, 2021 | - - |
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 15, 2020 | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 21, 2020 | This variant is associated with the following publications: (PMID: 30773290, 11223851, 25525159, 20378821) - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | COL4A5: BS2 - |
Autosomal dominant Alport syndrome Pathogenic:1
Pathogenic, flagged submission | literature only | Yale Center for Mendelian Genomics, Yale University | Feb 14, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 01, 2024 | Variant summary: COL4A5 c.2692A>G (p.Met898Val) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00022 in 1203910 control chromosomes, including 85 hemizygotes (gnomAD v4.1.0). c.2692A>G has been reported in the literature in individuals with clinical features of Alport syndrome (e.g., Barker_2001, Connaughton_2019, Uliana_2021), however these report(s) do not provide unequivocal conclusions about association of the variant with Alport Syndrome 1, X-Linked Recessive. Co-occurrences with other pathogenic variant(s) have been reported (INF2 c.353T>A, p.Ile118Asn), providing supporting evidence for a benign role (Connaughton_2019). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 11223851, 30773290, 33369211). ClinVar contains an entry for this variant (Variation ID: 24554). Based on the evidence outlined above, the variant was classified as likely benign. - |
COL4A5-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 15, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
.;T;T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
A;A
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.
REVEL
Uncertain
Sift
Benign
T;T;.
Sift4G
Benign
T;T;.
Polyphen
0.0050, 0.0030
.;B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
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