2-227027903-C-T

Position:

• chr2-227027903-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_000092.5(COL4A4):​c.4080G>A​(p.Pro1360Pro) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 1,601,552 control chromosomes in the GnomAD database, including 159,533 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.47 (16859 hom., cov: 31)
  • Exomes 𝑓: 0.44 (142674 hom.)
• Consequence: COL4A4 NM_000092.5 splice_region, synonymous
• Scores: Splicing: ADA: 0.0001429
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:11
• Conservation: PhyloP100: 0.529

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]

COL4A4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BP6: Variant 2-227027903-C-T is Benign according to our data. Variant chr2-227027903-C-T is described in ClinVar as [Benign]. Clinvar id is 255036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-227027903-C-T is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.529 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL4A4	NM_000092.5	c.4080G>A	p.Pro1360Pro	splice_region_variant, synonymous_variant	42/48	ENST00000396625.5	NP_000083.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL4A4	ENST00000396625.5	c.4080G>A	p.Pro1360Pro	splice_region_variant, synonymous_variant	42/48	5	NM_000092.5	ENSP00000379866.3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71052 AN: 151816 Hom.: 16825 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.439

GnomAD3 exomes AF: 0.472 AC: 117495 AN: 248986 Hom.: 28238 AF XY: 0.469 AC XY: 63418 AN XY: 135118

Gnomad AFR exome AF: 0.540

Gnomad AMR exome AF: 0.534

Gnomad ASJ exome AF: 0.510

Gnomad EAS exome AF: 0.398

Gnomad SAS exome AF: 0.552

Gnomad FIN exome AF: 0.499

Gnomad NFE exome AF: 0.426

Gnomad OTH exome AF: 0.455

GnomAD4 exome AF: 0.440 AC: 637409 AN: 1449618 Hom.: 142674 Cov.: 30 AF XY: 0.441 AC XY: 318677 AN XY: 721854

Gnomad4 AFR exome AF: 0.531

Gnomad4 AMR exome AF: 0.529

Gnomad4 ASJ exome AF: 0.516

Gnomad4 EAS exome AF: 0.403

Gnomad4 SAS exome AF: 0.553

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.442

GnomAD4 genome AF: 0.468 AC: 71131 AN: 151934 Hom.: 16859 Cov.: 31 AF XY: 0.470 AC XY: 34866 AN XY: 74258

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.433

Alfa AF: 0.431 Hom.: 15013

Bravo AF: 0.470

Asia WGS AF: 0.475 AC: 1656 AN: 3478

EpiCase AF: 0.403

EpiControl AF: 0.411

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:4

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 21, 2016	p.Pro1360Pro in exon 42 of COL4A4: This variant is not expected to have clinical significance because it has been identified in 55.67% (9183/16494) of South Asi an chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinsti tute.org; dbSNP rs2228556). -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jul 15, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 56% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 52. Only high quality variants are reported. -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 09, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 03, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Alport syndrome Benign:2

Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Benign familial hematuria;C4746745:Autosomal recessive Alport syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 14, 2021

- -

Autosomal recessive Alport syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	11
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00014
dbscSNV1_RF	Benign	0.026
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: rs2228556; hg19: chr2-227892619; COSMIC: COSV61632094;