NM_000093.5:c.4955-28T>C

Variant names:

• chr9-134825764-T-C
• rs7868111
• NM_000093.5:c.4955-28T>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000093.5(COL5A1):​c.4955-28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 1,488,796 control chromosomes in the GnomAD database, including 374,572 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.71 (38841 hom., cov: 33)
  • Exomes 𝑓: 0.71 (335731 hom.)
• Consequence: COL5A1 NM_000093.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -4.28

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]

LOC101448202 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 9-134825764-T-C is Benign according to our data. Variant chr9-134825764-T-C is described in ClinVar as [Benign]. Clinvar id is 255092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL5A1	NM_000093.5	c.4955-28T>C		intron_variant	Intron 62 of 65	ENST00000371817.8	NP_000084.3
COL5A1	NM_001278074.1	c.4955-28T>C		intron_variant	Intron 62 of 65		NP_001265003.1
COL5A1	XM_017014266.3	c.4955-28T>C		intron_variant	Intron 62 of 64		XP_016869755.1
LOC101448202	NR_103451.2	n.71-5555A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL5A1	ENST00000371817.8	c.4955-28T>C		intron_variant	Intron 62 of 65	1	NM_000093.5	ENSP00000360882.3
COL5A1	ENST00000371820.4	c.4955-28T>C		intron_variant	Intron 62 of 65	2		ENSP00000360885.4
COL5A1	ENST00000460264.5	n.423-28T>C		intron_variant	Intron 3 of 4	3
COL5A1	ENST00000465877.1	n.135-28T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108617 AN: 152074 Hom.: 38816 Cov.: 33

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.710

GnomAD3 exomes AF: 0.720 AC: 179176 AN: 248800 Hom.: 64616 AF XY: 0.726 AC XY: 97720 AN XY: 134560

Gnomad AFR exome AF: 0.731

Gnomad AMR exome AF: 0.661

Gnomad ASJ exome AF: 0.780

Gnomad EAS exome AF: 0.778

Gnomad SAS exome AF: 0.793

Gnomad FIN exome AF: 0.721

Gnomad NFE exome AF: 0.703

Gnomad OTH exome AF: 0.712

GnomAD4 exome AF: 0.708 AC: 945974 AN: 1336604 Hom.: 335731 Cov.: 18 AF XY: 0.710 AC XY: 477090 AN XY: 671614

Gnomad4 AFR exome AF: 0.736

Gnomad4 AMR exome AF: 0.665

Gnomad4 ASJ exome AF: 0.785

Gnomad4 EAS exome AF: 0.732

Gnomad4 SAS exome AF: 0.790

Gnomad4 FIN exome AF: 0.719

Gnomad4 NFE exome AF: 0.698

Gnomad4 OTH exome AF: 0.714

GnomAD4 genome AF: 0.714 AC: 108690 AN: 152192 Hom.: 38841 Cov.: 33 AF XY: 0.718 AC XY: 53389 AN XY: 74400

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.709

Alfa AF: 0.666 Hom.: 4084

Bravo AF: 0.715

Asia WGS AF: 0.786 AC: 2729 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fibromuscular dysplasia, multifocal Benign:1

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Ehlers-Danlos syndrome, classic type, 1 Benign:1

Jul 30, 2021

Genome-Nilou Lab

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	-0.90
CADD	Benign	0.37
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7868111; hg19: chr9-137717610;