NM_001854.4:c.106+702T>C

Variant names:

• chr1-103107371-A-G
• rs4338381
• NM_001854.4:c.106+702T>C

Variant summary

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

The NM_001854.4(COL11A1):​c.106+702T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 150,644 control chromosomes in the GnomAD database, including 9,361 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 0.35 (9361 hom., cov: 26)
• Consequence: COL11A1 NM_001854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

COL11A1 (HGNC:2186): (collagen type XI alpha 1 chain) This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4	c.106+702T>C		intron_variant	Intron 1 of 66	ENST00000370096.9	NP_001845.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9	c.106+702T>C		intron_variant	Intron 1 of 66	1	NM_001854.4	ENSP00000359114.3

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52512 AN: 150530 Hom.: 9357 Cov.: 26

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.349 AC: 52546 AN: 150644 Hom.: 9361 Cov.: 26 AF XY: 0.348 AC XY: 25535 AN XY: 73468

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.0910

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.303

Alfa AF: 0.338 Hom.: 4500

Bravo AF: 0.334

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.76

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: rs4338381; hg19: chr1-103572927;