chr1-102899209-A-T

Variant names:

• chr1-102899209-A-T
• rs1676500
• NM_001854.4:c.4087-215T>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001854.4(COL11A1):​c.4087-215T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 152,172 control chromosomes in the GnomAD database, including 703 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.088 (703 hom., cov: 32)
• Consequence: COL11A1 NM_001854.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.58

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-102899209-A-T is Benign according to our data. Variant chr1-102899209-A-T is described in ClinVar as [Benign]. Clinvar id is 1230519.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4	c.4087-215T>A		intron_variant	Intron 54 of 66	ENST00000370096.9	NP_001845.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9	c.4087-215T>A		intron_variant	Intron 54 of 66	1	NM_001854.4	ENSP00000359114.3

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13358 AN: 152056 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0558

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0878 AC: 13363 AN: 152172 Hom.: 703 Cov.: 32 AF XY: 0.0868 AC XY: 6457 AN XY: 74424

African (AFR) AF: 0.132 AC: 5475 AN: 41528

American (AMR) AF: 0.0743 AC: 1136 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.0668 AC: 346 AN: 5182

South Asian (SAS) AF: 0.0468 AC: 226 AN: 4830

European-Finnish (FIN) AF: 0.0558 AC: 590 AN: 10574

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.0695 AC: 4722 AN: 67986

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0767 Hom.: 55

Bravo AF: 0.0916

Asia WGS AF: 0.0540 AC: 188 AN: 3464

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.34
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

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Other links and lift over

dbSNP: rs1676500; hg19: chr1-103364765;