NM_004370.6:c.6848G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004370.6(COL12A1):c.6848G>A(p.Gly2283Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00211 in 1,613,300 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 25 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 26 hom. )

Consequence

COL12A1
NM_004370.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 5.18

Publications

8 publications found

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]

COL12A1 Gene-Disease associations (from GenCC):

Bethlem myopathy 2
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
Bethlem myopathy 2
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Illumina, Genomics England PanelApp
Ullrich congenital muscular dystrophy 2
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
Bethlem myopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Ullrich congenital muscular dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

COL12A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0063426495).

BP6

Variant 6-75123971-C-T is Benign according to our data. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-75123971-C-T is described in CliVar as Benign. Clinvar id is 475891.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0107 (1630/152250) while in subpopulation AFR AF = 0.0367 (1524/41542). AF 95% confidence interval is 0.0352. There are 25 homozygotes in GnomAd4. There are 776 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 25 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL12A1	NM_004370.6 link	c.6848G>A	p.Gly2283Glu	missense_variant	Exon 42 of 66	ENST00000322507.13	NP_004361.3	Q99715-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
COL12A1	ENST00000322507.13 link	c.6848G>A	p.Gly2283Glu	missense_variant	Exon 42 of 66	1	NM_004370.6	ENSP00000325146.8	Q99715-1
COL12A1	ENST00000345356.10 link	c.3356G>A	p.Gly1119Glu	missense_variant	Exon 27 of 51	1		ENSP00000305147.9	Q99715-2
COL12A1	ENST00000483888.6 link	c.6848G>A	p.Gly2283Glu	missense_variant	Exon 42 of 65	5		ENSP00000421216.1	D6RGG3
COL12A1	ENST00000416123.6 link	c.6848G>A	p.Gly2283Glu	missense_variant	Exon 41 of 63	5		ENSP00000412864.2	Q99715-4

Frequencies

GnomAD3 genomes

AF:

0.0107

AC:

1630

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0368

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00439

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000353

Gnomad OTH

AF:

0.00573

GnomAD2 exomes

AF:

0.00261

AC:

650

AN:

248698

AF XY:

0.00202

show subpopulations

Gnomad AFR exome

AF:

0.0342

Gnomad AMR exome

AF:

0.00212

Gnomad ASJ exome

AF:

0.0000995

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000355

Gnomad OTH exome

AF:

0.000829

GnomAD4 exome

AF:

0.00121

AC:

1774

AN:

1461050

Hom.:

Cov.:

AF XY:

0.00109

AC XY:

793

AN XY:

726694

show subpopulations

African (AFR)

AF:

0.0369

AC:

1235

AN:

33442

American (AMR)

AF:

0.00213

AC:

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26114

East Asian (EAS)

AF:

0.00

AC:

AN:

39666

South Asian (SAS)

AF:

0.000151

AC:

AN:

86202

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53396

Middle Eastern (MID)

AF:

0.00451

AC:

AN:

5760

European-Non Finnish (NFE)

AF:

0.000198

AC:

220

AN:

1111422

Other (OTH)

AF:

0.00306

AC:

185

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

169

254

338

423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

138

184

230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0107

AC:

1630

AN:

152250

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

776

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.0367

AC:

1524

AN:

41542

American (AMR)

AF:

0.00438

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000353

AC:

AN:

68014

Other (OTH)

AF:

0.00567

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

160

239

319

399

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00359

Hom.:

Bravo

AF:

0.0116

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.0344

AC:

128

ESP6500EA

AF:

0.000486

AC:

ExAC

AF:

0.00322

AC:

389

Asia WGS

AF:

0.00202

AC:

AN:

3476

EpiCase

AF:

0.000491

EpiControl

AF:

0.000712

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 15, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.44

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.033

T;T;.;.;.

Eigen

Uncertain

0.65

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.88

D;D;D;D;D

MetaRNN

Benign

0.0063

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

.;M;.;M;.

PhyloP100

5.2

PrimateAI

Uncertain

0.57

PROVEAN

Uncertain

-2.8

.;D;D;D;D

REVEL

Benign

0.16

Sift

Benign

0.041

.;D;D;D;D

Sift4G

Uncertain

0.0030

D;D;D;D;D

Polyphen

1.0, 1.0

.;D;D;.;.

Vest4

0.32

MVP

0.44

MPC

1.5

ClinPred

0.016

GERP RS

5.5

Varity_R

0.24

gMVP

0.79

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over