6-75152378-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_004370.6(COL12A1):​c.3670C>G​(p.Arg1224Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,368 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

COL12A1
NM_004370.6 missense

Scores

4
5
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.64
Variant links:
Genes affected
COL12A1 (HGNC:2188): (collagen type XII alpha 1 chain) This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.82

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL12A1NM_004370.6 linkc.3670C>G p.Arg1224Gly missense_variant Exon 18 of 66 ENST00000322507.13 NP_004361.3 Q99715-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL12A1ENST00000322507.13 linkc.3670C>G p.Arg1224Gly missense_variant Exon 18 of 66 1 NM_004370.6 ENSP00000325146.8 Q99715-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461368
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
727010
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Pathogenic
0.36
D
BayesDel_noAF
Pathogenic
0.28
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.018
T;T;.;.;.
Eigen
Benign
0.12
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.92
D;D;D;D;D
M_CAP
Benign
0.045
D
MetaRNN
Pathogenic
0.82
D;D;D;D;D
MetaSVM
Benign
-0.60
T
MutationAssessor
Benign
1.6
.;L;.;L;.
PrimateAI
Uncertain
0.66
T
PROVEAN
Benign
-2.2
.;N;N;N;N
REVEL
Uncertain
0.54
Sift
Benign
0.29
.;T;T;T;T
Sift4G
Benign
0.071
T;D;T;D;D
Polyphen
0.040, 0.0030
.;B;B;.;.
Vest4
0.80
MutPred
0.72
.;Loss of MoRF binding (P = 0.0251);.;Loss of MoRF binding (P = 0.0251);Loss of MoRF binding (P = 0.0251);
MVP
0.95
MPC
0.24
ClinPred
0.73
D
GERP RS
5.7
Varity_R
0.22
gMVP
0.84

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-75862094; API