rs10628678

chr9-134843171-T-TAGGG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000093.5(COL5A1):c.*870_*873dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 149,870 control chromosomes in the GnomAD database, including 33,320 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.66 (33260 hom., cov: 0)
  • Exomes 𝑓: 0.77 (60 hom.)
• Consequence: COL5A1 NM_000093.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.491

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 -10 ACMG points.

• BP6: Variant 9-134843171-T-TAGGG is Benign according to our data. Variant chr9-134843171-T-TAGGG is described in ClinVar as [Benign]. Clinvar id is 365764.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL5A1	NM_000093.5	c.*870_*873dup		3_prime_UTR_variant	66/66	ENST00000371817.8
LOC101448202	NR_103451.2	n.71-22963_71-22962insCCCT		intron_variant, non_coding_transcript_variant
COL5A1	NM_001278074.1	c.*870_*873dup		3_prime_UTR_variant	66/66

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL5A1	ENST00000371817.8	c.*870_*873dup		3_prime_UTR_variant	66/66	1	NM_000093.5	P4
COL5A1	ENST00000371820.4	c.*870_*873dup		3_prime_UTR_variant	66/66	2		A2

Frequencies

GnomAD3 genomes AF: 0.663 AC: 99225 AN: 149570 Hom.: 33246 Cov.: 0

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.676

GnomAD4 exome AF: 0.765 AC: 150 AN: 196 Hom.: 60 Cov.: 0 AF XY: 0.767 AC XY: 92 AN XY: 120

Gnomad4 FIN exome AF: 0.765

GnomAD4 genome AF: 0.663 AC: 99277 AN: 149674 Hom.: 33260 Cov.: 0 AF XY: 0.660 AC XY: 48056 AN XY: 72828

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.678

Alfa AF: 0.637 Hom.: 3161

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ehlers-Danlos syndrome type 7A Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10628678; hg19: chr9-137735017;