6-33168185-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080680.3(COL11A2):c.3961-333G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,736 control chromosomes in the GnomAD database, including 17,802 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (17802 hom., cov: 30)
• Consequence: COL11A2 NM_080680.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

Genes affected

COL11A2 (HGNC:2187): (collagen type XI alpha 2 chain) This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL11A2	NM_080680.3	c.3961-333G>C		intron_variant		ENST00000341947.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL11A2	ENST00000341947.7	c.3961-333G>C		intron_variant		5	NM_080680.3	P4
COL11A2	ENST00000374708.8	c.3703-333G>C		intron_variant		5		A1
COL11A2	ENST00000477772.1	n.273-2369G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72242 AN: 151614 Hom.: 17784 Cov.: 30

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.476 AC: 72300 AN: 151736 Hom.: 17802 Cov.: 30 AF XY: 0.477 AC XY: 35391 AN XY: 74156

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.524

Alfa AF: 0.299 Hom.: 736

Bravo AF: 0.498

Asia WGS AF: 0.549 AC: 1911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.6
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs986522; hg19: chr6-33135962;