6-70279648-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Variant names:

• chr6-70279648-C-CAAAAAAAAAAAAAAAAA
• rs57993118
• NM_001851.6:c.975+1147_975+1163dupTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS1

The NM_001851.6(COL9A1):​c.975+1147_975+1163dupTTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 20)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: COL9A1 NM_001851.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 0 publications found

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]

COL9A1 Gene-Disease associations (from GenCC):

• Stickler syndrome, type 4

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, ClinGen, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• epiphyseal dysplasia, multiple, 6

  Inheritance: Unknown, AD, AR Classification: DEFINITIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
• multiple epiphyseal dysplasia due to collagen 9 anomaly

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• autosomal recessive Stickler syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Stickler syndrome

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.000243 (14/57568) while in subpopulation AFR AF = 0.000669 (11/16432). AF 95% confidence interval is 0.000375. There are 0 homozygotes in GnomAd4. There are 8 alleles in the male GnomAd4 subpopulation. Median coverage is 20. This position passed quality control check.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001851.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL9A1	NM_001851.6	MANE Select	c.975+1147_975+1163dupTTTTTTTTTTTTTTTTT		intron	N/A	NP_001842.3
	COL9A1	NM_001377289.1		c.246+1147_246+1163dupTTTTTTTTTTTTTTTTT		intron	N/A	NP_001364218.1	A0A804HIB6
	COL9A1	NM_078485.4		c.246+1147_246+1163dupTTTTTTTTTTTTTTTTT		intron	N/A	NP_511040.2	P20849-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL9A1	ENST00000357250.11	TSL:1 MANE Select	c.975+1163_975+1164insTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000349790.6	P20849-1
	COL9A1	ENST00000320755.12	TSL:1	c.246+1163_246+1164insTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000315252.7	P20849-2
	COL9A1	ENST00000683980.2		c.246+1163_246+1164insTTTTTTTTTTTTTTTTT		intron	N/A	ENSP00000506990.1	A0A804HIB6

Frequencies

GnomAD3 genomes AF: 0.000243 AC: 14 AN: 57540 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000671

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000673

Gnomad EAS AF: 0.000466

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000348

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 676 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 372

African (AFR) AF: 0.00 AC: 0 AN: 30

American (AMR) AF: 0.00 AC: 0 AN: 24

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 32

East Asian (EAS) AF: 0.00 AC: 0 AN: 62

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 442

Other (OTH) AF: 0.00 AC: 0 AN: 48

GnomAD4 genome AF: 0.000243 AC: 14 AN: 57568 Hom.: 0 Cov.: 20 AF XY: 0.000303 AC XY: 8 AN XY: 26412

African (AFR) AF: 0.000669 AC: 11 AN: 16432

American (AMR) AF: 0.00 AC: 0 AN: 4676

Ashkenazi Jewish (ASJ) AF: 0.000673 AC: 1 AN: 1486

East Asian (EAS) AF: 0.000467 AC: 1 AN: 2140

South Asian (SAS) AF: 0.00 AC: 0 AN: 1306

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 72

European-Non Finnish (NFE) AF: 0.0000348 AC: 1 AN: 28722

Other (OTH) AF: 0.00 AC: 0 AN: 716

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs57993118; hg19: chr6-70989351;