rs1415363

Positions:

• chr1-103087379-A-G
• chr1-103087379-A-T

Variant summary

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

The NM_001854.4(COL11A1):​c.107-4407T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 152,142 control chromosomes in the GnomAD database, including 47,891 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 0.79 (47891 hom., cov: 32)
• Consequence: COL11A1 NM_001854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL11A1	NM_001854.4	c.107-4407T>C		intron_variant		ENST00000370096.9	NP_001845.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9	c.107-4407T>C		intron_variant		1	NM_001854.4	ENSP00000359114	P1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120250 AN: 152024 Hom.: 47851 Cov.: 32

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.791 AC: 120347 AN: 152142 Hom.: 47891 Cov.: 32 AF XY: 0.790 AC XY: 58742 AN XY: 74364

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.743

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.812

Alfa AF: 0.766 Hom.: 58607

Bravo AF: 0.802

Asia WGS AF: 0.900 AC: 3126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.80

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: rs1415363; hg19: chr1-103552935;