GeneBe

rs397867048

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001379500.1(COL18A1):​c.2577+36_2577+37delCC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

COL18A1
NM_001379500.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.56

Publications

2 publications found
Variant links:
Genes affected
COL18A1 (HGNC:2195): (collagen type XVIII alpha 1 chain) This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
SLC19A1 (HGNC:10937): (solute carrier family 19 member 1) The membrane protein encoded by this gene is a transporter of folate and is involved in the regulation of intracellular concentrations of folate. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2011]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001379500.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
COL18A1
NM_001379500.1
MANE Select
c.2577+36_2577+37delCC
intron
N/ANP_001366429.1
COL18A1
NM_130444.3
c.3822+36_3822+37delCC
intron
N/ANP_569711.2
COL18A1
NM_030582.4
c.3117+36_3117+37delCC
intron
N/ANP_085059.2

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
COL18A1
ENST00000651438.1
MANE Select
c.2577+35_2577+36delCC
intron
N/AENSP00000498485.1
COL18A1
ENST00000355480.10
TSL:1
c.3117+35_3117+36delCC
intron
N/AENSP00000347665.5
SLC19A1
ENST00000417954.5
TSL:1
c.763-225_763-224delGG
intron
N/AENSP00000393988.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
828092
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
436910
African (AFR)
AF:
0.00
AC:
0
AN:
21224
American (AMR)
AF:
0.00
AC:
0
AN:
43970
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22276
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36946
South Asian (SAS)
AF:
0.00
AC:
0
AN:
73796
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51746
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4210
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
534492
Other (OTH)
AF:
0.00
AC:
0
AN:
39432
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
-2.6

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

Other links and lift over

dbSNP: rs397867048; hg19: chr21-46916516; API