rs5929098

Variant names:

• chrX-108449075-C-G
• rs5929098
• NM_033380.3:c.81+8869C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-108449075-C-G
• chrX-108449075-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_033380.3(COL4A5):​c.81+8869C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 23)
• Consequence: COL4A5 NM_033380.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL4A5	NM_033380.3	c.81+8869C>G		intron_variant	Intron 1 of 52	ENST00000328300.11	NP_203699.1
COL4A5	NM_000495.5	c.81+8869C>G		intron_variant	Intron 1 of 50		NP_000486.1
COL4A5	XM_047441810.1	c.-296+8869C>G		intron_variant	Intron 1 of 53		XP_047297766.1
COL4A5	XM_047441811.1	c.81+8869C>G		intron_variant	Intron 1 of 41		XP_047297767.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL4A5	ENST00000328300.11	c.81+8869C>G		intron_variant	Intron 1 of 52	1	NM_033380.3	ENSP00000331902.7
COL4A5	ENST00000361603.7	c.81+8869C>G		intron_variant	Intron 1 of 50	2		ENSP00000354505.2
COL4A5	ENST00000470339.1	n.265+8869C>G		intron_variant	Intron 1 of 5	3
COL4A5	ENST00000642185.1	n.*122+8571C>G		intron_variant	Intron 2 of 2			ENSP00000495101.1

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.50

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: rs5929098; hg19: chrX-107692305;