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GeneBe

rs10858286

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000093.5(COL5A1):c.5370+3334C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,998 control chromosomes in the GnomAD database, including 23,412 homozygotes. 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: 𝑓 0.55 ( 23412 hom., cov: 32)

Consequence

COL5A1
NM_000093.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21
Variant links:
Genes affected
COL5A1 (HGNC:2209): (collagen type V alpha 1 chain) This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COL5A1NM_000093.5 linkuse as main transcriptc.5370+3334C>T intron_variant ENST00000371817.8
LOC101448202NR_103451.2 linkuse as main transcriptn.71-18329G>A intron_variant, non_coding_transcript_variant
COL5A1NM_001278074.1 linkuse as main transcriptc.5370+3334C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COL5A1ENST00000371817.8 linkuse as main transcriptc.5370+3334C>T intron_variant 1 NM_000093.5 P4P20908-1
COL5A1ENST00000371820.4 linkuse as main transcriptc.5370+3334C>T intron_variant 2 A2P20908-2

Frequencies

GnomAD3 genomes
AF:
0.546
AC:
82972
AN:
151880
Hom.:
23412
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.437
Gnomad AMI
AF:
0.573
Gnomad AMR
AF:
0.475
Gnomad ASJ
AF:
0.621
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.555
Gnomad FIN
AF:
0.535
Gnomad MID
AF:
0.668
Gnomad NFE
AF:
0.638
Gnomad OTH
AF:
0.547
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.546
AC:
82987
AN:
151998
Hom.:
23412
Cov.:
32
AF XY:
0.537
AC XY:
39917
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.436
Gnomad4 AMR
AF:
0.475
Gnomad4 ASJ
AF:
0.621
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.555
Gnomad4 FIN
AF:
0.535
Gnomad4 NFE
AF:
0.638
Gnomad4 OTH
AF:
0.547
Alfa
AF:
0.621
Hom.:
31805
Bravo
AF:
0.533
Asia WGS
AF:
0.469
AC:
1628
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
0.27
Dann
Benign
0.57

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10858286; hg19: chr9-137730384; COSMIC: COSV65667232; COSMIC: COSV65667232; API