X-108599764-C-T

Variant names:

• chrX-108599764-C-T
• rs5973838
• NM_033380.3:c.1948+894C>T

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BS2_Supporting

The NM_033380.3(COL4A5):​c.1948+894C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 112,118 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.000027 (0 hom., 2 hem., cov: 23)
• Consequence: COL4A5 NM_033380.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.621
• Publications: 0 publications found

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]

COL4A5 Gene-Disease associations (from GenCC):

• Alport syndrome

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen, G2P
• X-linked Alport syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Genomics England PanelApp, Myriad Women’s Health, Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant X-108599764-C-T is Benign according to our data. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-108599764-C-T is described in CliVar as Benign. Clinvar id is 2883985.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd4 at 2 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL4A5	NM_033380.3	c.1948+894C>T		intron_variant	Intron 25 of 52	ENST00000328300.11	NP_203699.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL4A5	ENST00000328300.11	c.1948+894C>T		intron_variant	Intron 25 of 52	1	NM_033380.3	ENSP00000331902.7
COL4A5	ENST00000483338.1	c.772+894C>T		intron_variant	Intron 9 of 19	1		ENSP00000495685.1
COL4A5	ENST00000361603.7	c.1948+894C>T		intron_variant	Intron 25 of 50	2		ENSP00000354505.2

Frequencies

GnomAD3 genomes AF: 0.0000268 AC: 3 AN: 112118 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000563

Gnomad OTH AF: 0.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0000268 AC: 3 AN: 112118 Hom.: 0 Cov.: 23 AF XY: 0.0000583 AC XY: 2 AN XY: 34304

African (AFR) AF: 0.00 AC: 0 AN: 30858

American (AMR) AF: 0.00 AC: 0 AN: 10552

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2647

East Asian (EAS) AF: 0.00 AC: 0 AN: 3591

South Asian (SAS) AF: 0.00 AC: 0 AN: 2691

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6092

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.0000563 AC: 3 AN: 53249

Other (OTH) AF: 0.00 AC: 0 AN: 1513

Alfa AF: 0.000230 Hom.: 2

Bravo AF: 0.0000189

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-0.62

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

Other links and lift over

dbSNP: rs5973838; hg19: chrX-107842994;