6-70216654-CT-C

Position:

• chr6-70216654-CT-C

Variant summary

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

The NM_001851.6(COL9A1):​c.*242del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: COL9A1 NM_001851.6 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.00

Genes affected

COL9A1 (HGNC:2217): (collagen type IX alpha 1 chain) This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-70216654-CT-C is Benign according to our data. Variant chr6-70216654-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1189526.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL9A1	NM_001851.6	c.*242del		3_prime_UTR_variant	38/38	ENST00000357250.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL9A1	ENST00000357250.11	c.*242del		3_prime_UTR_variant	38/38	1	NM_001851.6	P1

Frequencies

GnomAD3 genomes AF: 0.00209 AC: 304 AN: 145542 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000759

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00129

Gnomad ASJ AF: 0.00176

Gnomad EAS AF: 0.000805

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.00671

Gnomad NFE AF: 0.00213

Gnomad OTH AF: 0.00299

GnomAD4 exome AF: 0.176 AC: 56254 AN: 318856 Hom.: 0 Cov.: 0 AF XY: 0.179 AC XY: 29979 AN XY: 167542

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.152

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.141

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.154

Gnomad4 NFE exome AF: 0.176

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.00211 AC: 307 AN: 145584 Hom.: 0 Cov.: 0 AF XY: 0.00252 AC XY: 178 AN XY: 70672

Gnomad4 AFR AF: 0.000833

Gnomad4 AMR AF: 0.00129

Gnomad4 ASJ AF: 0.00176

Gnomad4 EAS AF: 0.000807

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.00213

Gnomad4 OTH AF: 0.00298

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs3215859; hg19: chr6-70926357;