1-102938828-T-C

Position:

• chr1-102938828-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001854.4(COL11A1):​c.3438+207A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 151,924 control chromosomes in the GnomAD database, including 30,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.63 (30554 hom., cov: 31)
• Consequence: COL11A1 NM_001854.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.533

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-102938828-T-C is Benign according to our data. Variant chr1-102938828-T-C is described in ClinVar as [Benign]. Clinvar id is 1282812.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL11A1	NM_001854.4	c.3438+207A>G		intron_variant		ENST00000370096.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL11A1	ENST00000370096.9	c.3438+207A>G		intron_variant		1	NM_001854.4	P1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95492 AN: 151806 Hom.: 30542 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.629 AC: 95543 AN: 151924 Hom.: 30554 Cov.: 31 AF XY: 0.629 AC XY: 46686 AN XY: 74246

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.631

Alfa AF: 0.651 Hom.: 41979

Bravo AF: 0.627

Asia WGS AF: 0.782 AC: 2700 AN: 3452

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.78

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: rs2126643; hg19: chr1-103404384; COSMIC: COSV62177053;