rs10484915

Variant summary

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

The NM_004370.6(COL12A1):​c.2710+1689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,234 control chromosomes in the GnomAD database, including 709 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 0.074 ( 709 hom., cov: 32)

Consequence

COL12A1
NM_004370.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.04
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COL12A1NM_004370.6 linkuse as main transcriptc.2710+1689A>G intron_variant ENST00000322507.13

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COL12A1ENST00000322507.13 linkuse as main transcriptc.2710+1689A>G intron_variant 1 NM_004370.6 P4Q99715-1
COL12A1ENST00000345356.10 linkuse as main transcriptc.74-20867A>G intron_variant 1 Q99715-2
COL12A1ENST00000416123.6 linkuse as main transcriptc.2710+1689A>G intron_variant 5 Q99715-4
COL12A1ENST00000483888.6 linkuse as main transcriptc.2710+1689A>G intron_variant 5 A1

Frequencies

GnomAD3 genomes
AF:
0.0736
AC:
11196
AN:
152116
Hom.:
690
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.139
Gnomad AMI
AF:
0.0164
Gnomad AMR
AF:
0.0875
Gnomad ASJ
AF:
0.0562
Gnomad EAS
AF:
0.222
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.0282
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0251
Gnomad OTH
AF:
0.0700
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0740
AC:
11262
AN:
152234
Hom.:
709
Cov.:
32
AF XY:
0.0760
AC XY:
5656
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.140
Gnomad4 AMR
AF:
0.0883
Gnomad4 ASJ
AF:
0.0562
Gnomad4 EAS
AF:
0.222
Gnomad4 SAS
AF:
0.120
Gnomad4 FIN
AF:
0.0282
Gnomad4 NFE
AF:
0.0251
Gnomad4 OTH
AF:
0.0683
Alfa
AF:
0.0531
Hom.:
55
Bravo
AF:
0.0814
Asia WGS
AF:
0.164
AC:
570
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.054
DANN
Benign
0.45

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: rs10484915; hg19: chr6-75883065; API