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GeneBe

9-134738722-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000093.5(COL5A1):c.1432-24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 1,595,100 control chromosomes in the GnomAD database, including 212,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 25568 hom., cov: 32)
Exomes 𝑓: 0.50 ( 186627 hom. )

Consequence

COL5A1
NM_000093.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.644
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 9-134738722-C-T is Benign according to our data. Variant chr9-134738722-C-T is described in ClinVar as [Benign]. Clinvar id is 255050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COL5A1NM_000093.5 linkuse as main transcriptc.1432-24C>T intron_variant ENST00000371817.8
COL5A1NM_001278074.1 linkuse as main transcriptc.1432-24C>T intron_variant
COL5A1XM_017014266.3 linkuse as main transcriptc.1432-24C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COL5A1ENST00000371817.8 linkuse as main transcriptc.1432-24C>T intron_variant 1 NM_000093.5 P4P20908-1
COL5A1ENST00000371820.4 linkuse as main transcriptc.1432-24C>T intron_variant 2 A2P20908-2

Frequencies

GnomAD3 genomes
AF:
0.563
AC:
85467
AN:
151810
Hom.:
25539
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.774
Gnomad AMI
AF:
0.626
Gnomad AMR
AF:
0.371
Gnomad ASJ
AF:
0.337
Gnomad EAS
AF:
0.503
Gnomad SAS
AF:
0.483
Gnomad FIN
AF:
0.503
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.511
Gnomad OTH
AF:
0.500
GnomAD3 exomes
AF:
0.480
AC:
120013
AN:
250028
Hom.:
31025
AF XY:
0.481
AC XY:
64988
AN XY:
135150
show subpopulations
Gnomad AFR exome
AF:
0.789
Gnomad AMR exome
AF:
0.252
Gnomad ASJ exome
AF:
0.329
Gnomad EAS exome
AF:
0.521
Gnomad SAS exome
AF:
0.483
Gnomad FIN exome
AF:
0.505
Gnomad NFE exome
AF:
0.508
Gnomad OTH exome
AF:
0.451
GnomAD4 exome
AF:
0.503
AC:
725521
AN:
1443172
Hom.:
186627
Cov.:
31
AF XY:
0.502
AC XY:
360654
AN XY:
719010
show subpopulations
Gnomad4 AFR exome
AF:
0.788
Gnomad4 AMR exome
AF:
0.266
Gnomad4 ASJ exome
AF:
0.326
Gnomad4 EAS exome
AF:
0.518
Gnomad4 SAS exome
AF:
0.483
Gnomad4 FIN exome
AF:
0.506
Gnomad4 NFE exome
AF:
0.509
Gnomad4 OTH exome
AF:
0.499
GnomAD4 genome
AF:
0.563
AC:
85542
AN:
151928
Hom.:
25568
Cov.:
32
AF XY:
0.555
AC XY:
41217
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.774
Gnomad4 AMR
AF:
0.371
Gnomad4 ASJ
AF:
0.337
Gnomad4 EAS
AF:
0.504
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.503
Gnomad4 NFE
AF:
0.511
Gnomad4 OTH
AF:
0.497
Alfa
AF:
0.499
Hom.:
24435
Bravo
AF:
0.562
Asia WGS
AF:
0.467
AC:
1629
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Fibromuscular dysplasia, multifocal Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabMar 15, 2022- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 18, 2018This 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. -
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabMar 15, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
0.82
Dann
Benign
0.38

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: rs3109677; hg19: chr9-137630568; COSMIC: COSV65669563; API