1-102887439-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001854.4(COL11A1):​c.4609-383G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,966 control chromosomes in the GnomAD database, including 21,790 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 0.49 ( 21790 hom., cov: 32)

Consequence

COL11A1
NM_001854.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.966
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL11A1NM_001854.4 linkc.4609-383G>A intron_variant ENST00000370096.9 NP_001845.3 P12107-1Q59HB5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL11A1ENST00000370096.9 linkc.4609-383G>A intron_variant 1 NM_001854.4 ENSP00000359114.3 P12107-1

Frequencies

GnomAD3 genomes
AF:
0.490
AC:
74339
AN:
151848
Hom.:
21778
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.138
Gnomad AMI
AF:
0.636
Gnomad AMR
AF:
0.656
Gnomad ASJ
AF:
0.564
Gnomad EAS
AF:
0.665
Gnomad SAS
AF:
0.570
Gnomad FIN
AF:
0.640
Gnomad MID
AF:
0.554
Gnomad NFE
AF:
0.617
Gnomad OTH
AF:
0.521
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.489
AC:
74358
AN:
151966
Hom.:
21790
Cov.:
32
AF XY:
0.496
AC XY:
36860
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.138
Gnomad4 AMR
AF:
0.657
Gnomad4 ASJ
AF:
0.564
Gnomad4 EAS
AF:
0.665
Gnomad4 SAS
AF:
0.570
Gnomad4 FIN
AF:
0.640
Gnomad4 NFE
AF:
0.617
Gnomad4 OTH
AF:
0.525
Alfa
AF:
0.536
Hom.:
2909
Bravo
AF:
0.477
Asia WGS
AF:
0.590
AC:
2035
AN:
3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.42
DANN
Benign
0.38

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

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

Other links and lift over

dbSNP: rs11164630; hg19: chr1-103352995; COSMIC: COSV62176893; COSMIC: COSV62176893; API