2-227008067-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_000092.5(COL4A4):c.4760C>G(p.Pro1587Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,613,882 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1587L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0021 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0036 (16 hom.)
• Consequence: COL4A4 NM_000092.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4 B:7
• Conservation: PhyloP100: 0.778

Genes affected

COL4A4 (HGNC:2206): (collagen type IV alpha 4 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. This particular collagen IV subunit, however, is only found in a subset of basement membranes. 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. Mutations in this gene are associated with type II autosomal recessive Alport syndrome (hereditary glomerulonephropathy) and with familial benign hematuria (thin basement membrane disease). Two transcripts, differing only in their transcription start sites, have been identified for this gene and, as is common for collagen genes, multiple polyadenylation sites are found in the 3' UTR. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.030847788).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00213 (324/152350) while in subpopulation NFE AF= 0.00367 (250/68032). AF 95% confidence interval is 0.0033. There are 1 homozygotes in gnomad4. There are 142 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome at 2 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A4	NM_000092.5	c.4760C>G	p.Pro1587Arg	missense_variant	47/48	ENST00000396625.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A4	ENST00000396625.5	c.4760C>G	p.Pro1587Arg	missense_variant	47/48	5	NM_000092.5	P1
COL4A4	ENST00000682098.1	c.362C>G	p.Pro121Arg	missense_variant	2/3

Frequencies

GnomAD3 genomes AF: 0.00213 AC: 324 AN: 152232 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.000675

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00367

Gnomad OTH AF: 0.00382

GnomAD3 exomes AF: 0.00203 AC: 504 AN: 248148 Hom.: 2 AF XY: 0.00207 AC XY: 279 AN XY: 134760

Gnomad AFR exome AF: 0.000392

Gnomad AMR exome AF: 0.000522

Gnomad ASJ exome AF: 0.00189

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00186

Gnomad FIN exome AF: 0.000470

Gnomad NFE exome AF: 0.00338

Gnomad OTH exome AF: 0.00216

GnomAD4 exome AF: 0.00356 AC: 5201 AN: 1461532 Hom.: 16 Cov.: 32 AF XY: 0.00340 AC XY: 2473 AN XY: 727072

Gnomad4 AFR exome AF: 0.000717

Gnomad4 AMR exome AF: 0.000537

Gnomad4 ASJ exome AF: 0.00199

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.00150

Gnomad4 FIN exome AF: 0.000433

Gnomad4 NFE exome AF: 0.00427

Gnomad4 OTH exome AF: 0.00315

GnomAD4 genome AF: 0.00213 AC: 324 AN: 152350 Hom.: 1 Cov.: 33 AF XY: 0.00191 AC XY: 142 AN XY: 74504

Gnomad4 AFR AF: 0.000673

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.000188

Gnomad4 NFE AF: 0.00367

Gnomad4 OTH AF: 0.00378

Alfa AF: 0.00278 Hom.: 0

Bravo AF: 0.00221

TwinsUK AF: 0.00512 AC: 19

ALSPAC AF: 0.00363 AC: 14

ESP6500AA AF: 0.000771 AC: 3

ESP6500EA AF: 0.00326 AC: 27

ExAC AF: 0.00179 AC: 217

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.00305

EpiControl AF: 0.00332

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:4 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2 Benign:3

Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The COL4A4 p.Pro1587Arg variant was identified in the literature however the frequency of this variant in an affected population was not provided. The variant was found in 1/11 families with Alport syndrome in the proband and two brothers all affected with haematuria and proteinuria as well as the father who was affected with end-stage renal disease (Mencarelli_2015_PMID: 25575550). This family also carried another variant in COL4A4 (c.1623+5G>T) and a variant in COL4A5 (p.Gly684Val), which the authors suggested may have led to a triallelic form of digenic inheritance of the renal phenotype observed in this family (Mencarelli_2015_PMID: 25575550). The p.P1587R variant was also found in a male proband, age 75, with hereditary nephritis who also had a variant in the COL4A3 gene (Chatterjee_2013_PMID: 24130771). The proband’s brother and sister had end stage renal disease related to presumed hereditary nephritis, however they were not tested for the variant (Chatterjee_2013_PMID: 24130771). The variant was also identified in dbSNP (ID: rs190148408), ClinVar (classified as a VUS by Athena Diagnostics), Cosmic (FATHMM prediction of neutral; score=0.42) and LOVD 3.0 (reported as likely pathogenic in 3 patients with Alport Syndrome, and as VUS in 6 patients with Alport Syndrome). The variant was identified in control databases in 575 of 279544 chromosomes (2 homozygous) at a frequency of 0.002057 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 438 of 127990 chromosomes (freq: 0.003422), Other in 16 of 7120 chromosomes (freq: 0.002247), South Asian in 57 of 30568 chromosomes (freq: 0.001865), Ashkenazi Jewish in 19 of 10348 chromosomes (freq: 0.001836), African in 14 of 24012 chromosomes (freq: 0.000583), Latino in 19 of 35320 chromosomes (freq: 0.000538) and European (Finnish) in 12 of 24740 chromosomes (freq: 0.000485); it was not observed in the East Asian populations. The p.Pro1587 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 05, 2019	This variant is associated with the following publications: (PMID: 28780565, 25575550, 24130771, 29924831, 30467950) -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 17, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2023	COL4A4: BS2 -

Alport syndrome Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Likely benign, no assertion criteria provided	clinical testing	Natera, Inc.	Apr 03, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Dec 12, 2022	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 04, 2018	p.Pro1587Arg in exon 47 of COL4A4: This variant is classified as likely benign, because although it has been reported in 3 individuals with features of Alport s yndrome (Chatterjee 2013, Mencarelli 2015, Sen 2017), it is present in 0.34% (43 0/126088) of European chromosomes by the Genome Aggregation Database (gnomAD, ht tp://gnomad.broadinstitute.org; dbSNP rs190148408). This allele frequency is too high to cause Alport syndrome or hearing loss due to the COL4A4 gene. ACMG/AMP criteria applied: BS1. -
Likely benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 24, 2019	- -

COL4A4-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 25, 2020

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.12
Cadd	Benign	17
Dann	Benign	0.22
DEOGEN2	Uncertain	0.42	T
Eigen	Benign	-0.13
Eigen_PC	Benign	-0.18
FATHMM_MKL	Benign	0.42	N
LIST_S2	Benign	0.84	T
M_CAP	Uncertain	0.27	D
MetaRNN	Benign	0.031	T
MetaSVM	Uncertain	-0.054	T
MutationAssessor	Benign	1.7	L
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-2.3	N
REVEL	Uncertain	0.33
Sift	Benign	0.90	T
Sift4G	Benign	0.79	T
Polyphen		0.91	P
Vest4		0.43
MVP		0.77
MPC		0.15
ClinPred		0.049	T
GERP RS		5.0
Varity_R		0.33
gMVP		0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs190148408; hg19: chr2-227872783; COSMIC: COSV61635993;