Genetic Variant NM_001854.4:c.1792-15_1792-10delATGATG (chr1-103005900-CCATCAT-C) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_001854.4(COL11A1):c.1792-15_1792-10delATGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00756 in 1,336,324 control chromosomes in the GnomAD database, including 93 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 49 hom., cov: 0)

Exomes 𝑓: 0.0068 ( 44 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 2.41

Variant links:

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]

COL11A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-103005900-CCATCAT-C is Benign according to our data. Variant chr1-103005900-CCATCAT-C is described in ClinVar as [Benign]. Clinvar id is 291531.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-103005900-CCATCAT-C is described in Lovd as [Benign]. Variant chr1-103005900-CCATCAT-C is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0138 (2077/150322) while in subpopulation AFR AF= 0.0431 (1765/40982). AF 95% confidence interval is 0.0414. There are 49 homozygotes in gnomad4. There are 987 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 49 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4 link	c.1792-15_1792-10delATGATG		intron_variant	Intron 17 of 66	ENST00000370096.9	NP_001845.3	P12107-1Q59HB5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9 link	c.1792-15_1792-10delATGATG		intron_variant	Intron 17 of 66	1	NM_001854.4	ENSP00000359114.3		P12107-1

Frequencies

GnomAD3 genomes

AF:

0.0138

AC:

2073

AN:

150208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0430

Gnomad AMI

AF:

0.00111

Gnomad AMR

AF:

0.00460

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.000395

Gnomad SAS

AF:

0.00232

Gnomad FIN

AF:

0.00284

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00274

Gnomad OTH

AF:

0.00778

GnomAD3 exomes

AF:

0.00707

AC:

1380

AN:

195300

Hom.:

AF XY:

0.00601

AC XY:

632

AN XY:

105128

show subpopulations

Gnomad AFR exome

AF:

0.0488

Gnomad AMR exome

AF:

0.00455

Gnomad ASJ exome

AF:

0.000611

Gnomad EAS exome

AF:

0.00146

Gnomad SAS exome

AF:

0.00334

Gnomad FIN exome

AF:

0.00419

Gnomad NFE exome

AF:

0.00413

Gnomad OTH exome

AF:

0.00678

GnomAD4 exome

AF:

0.00677

AC:

8031

AN:

1186002

Hom.:

AF XY:

0.00627

AC XY:

3698

AN XY:

589506

show subpopulations

Gnomad4 AFR exome

AF:

0.0464

Gnomad4 AMR exome

AF:

0.00470

Gnomad4 ASJ exome

AF:

0.00106

Gnomad4 EAS exome

AF:

0.00184

Gnomad4 SAS exome

AF:

0.00455

Gnomad4 FIN exome

AF:

0.00458

Gnomad4 NFE exome

AF:

0.00599

Gnomad4 OTH exome

AF:

0.00793

GnomAD4 genome

AF:

0.0138

AC:

2077

AN:

150322

Hom.:

Cov.:

AF XY:

0.0135

AC XY:

987

AN XY:

73256

show subpopulations

Gnomad4 AFR

AF:

0.0431

Gnomad4 AMR

AF:

0.00452

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.000396

Gnomad4 SAS

AF:

0.00211

Gnomad4 FIN

AF:

0.00284

Gnomad4 NFE

AF:

0.00274

Gnomad4 OTH

AF:

0.00770

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics, Academic Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:2

May 21, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Marshall syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fibrochondrogenesis 1

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Stickler Syndrome, Dominant

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over