9-134844804-T-C

Position:

• chr9-134844804-T-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.*2501T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,154 control chromosomes in the GnomAD database, including 31,371 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.63 (31371 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: COL5A1 NM_000093.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0360

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=-0.63).
• BP6: Variant 9-134844804-T-C is Benign according to our data. Variant chr9-134844804-T-C is described in ClinVar as [Benign]. Clinvar id is 365795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL5A1	NM_000093.5	c.*2501T>C		3_prime_UTR_variant	66/66	ENST00000371817.8	NP_000084.3
COL5A1	NM_001278074.1	c.*2501T>C		3_prime_UTR_variant	66/66		NP_001265003.1
LOC101448202	NR_103451.2	n.71-24595A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL5A1	ENST00000371817.8	c.*2501T>C		3_prime_UTR_variant	66/66	1	NM_000093.5	ENSP00000360882.3
COL5A1	ENST00000371820.4	c.*2501T>C		3_prime_UTR_variant	66/66	2		ENSP00000360885.4

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96414 AN: 152036 Hom.: 31362 Cov.: 34

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.661

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.634 AC: 96459 AN: 152154 Hom.: 31371 Cov.: 34 AF XY: 0.632 AC XY: 46969 AN XY: 74372

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.664

Alfa AF: 0.693 Hom.: 48855

Bravo AF: 0.613

Asia WGS AF: 0.560 AC: 1947 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ehlers-Danlos syndrome type 7A Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.6
DANN	Benign	0.75

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: rs3128575; hg19: chr9-137736650;