1-103017958-C-T

Variant names:

• chr1-103017958-C-T
• rs945748
• NM_001854.4:c.1351-76G>A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001854.4(COL11A1):​c.1351-76G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 1,160,478 control chromosomes in the GnomAD database, including 285,780 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.60 (30128 hom., cov: 31)
  • Exomes 𝑓: 0.71 (255652 hom.)
• Consequence: COL11A1 NM_001854.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.203

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-103017958-C-T is Benign according to our data. Variant chr1-103017958-C-T is described in ClinVar as [Benign]. Clinvar id is 674750.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4	c.1351-76G>A		intron_variant	Intron 10 of 66	ENST00000370096.9	NP_001845.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9	c.1351-76G>A		intron_variant	Intron 10 of 66	1	NM_001854.4	ENSP00000359114.3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90844 AN: 151750 Hom.: 30126 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.625

GnomAD4 exome AF: 0.706 AC: 712579 AN: 1008610 Hom.: 255652 AF XY: 0.712 AC XY: 371691 AN XY: 522036

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.693

Gnomad4 ASJ exome AF: 0.663

Gnomad4 EAS exome AF: 0.926

Gnomad4 SAS exome AF: 0.826

Gnomad4 FIN exome AF: 0.699

Gnomad4 NFE exome AF: 0.701

Gnomad4 OTH exome AF: 0.689

GnomAD4 genome AF: 0.598 AC: 90861 AN: 151868 Hom.: 30128 Cov.: 31 AF XY: 0.605 AC XY: 44950 AN XY: 74238

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.627

Alfa AF: 0.691 Hom.: 45189

Bravo AF: 0.581

Asia WGS AF: 0.814 AC: 2831 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.58

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: rs945748; hg19: chr1-103483514; COSMIC: COSV62177179;