rs181257320

chr6-75151862-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PP3_Strong BP6_Very_Strong BS1 BS2

The NM_004370.6(COL12A1):c.4000+5G>A variant causes a splice donor 5th base, intron change. The variant allele was found at a frequency of 0.00371 in 1,613,108 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0033 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0037 (9 hom.)
• Consequence: COL12A1 NM_004370.6 splice_donor_5th_base, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 5.54

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• BP6: Variant 6-75151862-C-T is Benign according to our data. Variant chr6-75151862-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 475863.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00333 (507/152146) while in subpopulation NFE AF= 0.00435 (296/68002). AF 95% confidence interval is 0.00394. There are 4 homozygotes in gnomad4. There are 261 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL12A1	NM_004370.6	c.4000+5G>A		splice_donor_5th_base_variant, intron_variant		ENST00000322507.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL12A1	ENST00000322507.13	c.4000+5G>A		splice_donor_5th_base_variant, intron_variant		1	NM_004370.6	P4

Frequencies

GnomAD3 genomes AF: 0.00333 AC: 506 AN: 152028 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00157

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00443

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00435

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00277 AC: 688 AN: 248576 Hom.: 0 AF XY: 0.00279 AC XY: 376 AN XY: 134828

Gnomad AFR exome AF: 0.00246

Gnomad AMR exome AF: 0.000493

Gnomad ASJ exome AF: 0.00559

Gnomad EAS exome AF: 0.0000556

Gnomad SAS exome AF: 0.00128

Gnomad FIN exome AF: 0.00462

Gnomad NFE exome AF: 0.00374

Gnomad OTH exome AF: 0.00282

GnomAD4 exome AF: 0.00375 AC: 5473 AN: 1460962 Hom.: 9 Cov.: 31 AF XY: 0.00377 AC XY: 2741 AN XY: 726788

Gnomad4 AFR exome AF: 0.00272

Gnomad4 AMR exome AF: 0.000716

Gnomad4 ASJ exome AF: 0.00521

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00118

Gnomad4 FIN exome AF: 0.00540

Gnomad4 NFE exome AF: 0.00413

Gnomad4 OTH exome AF: 0.00364

GnomAD4 genome AF: 0.00333 AC: 507 AN: 152146 Hom.: 4 Cov.: 32 AF XY: 0.00351 AC XY: 261 AN XY: 74386

Gnomad4 AFR AF: 0.00263

Gnomad4 AMR AF: 0.00157

Gnomad4 ASJ AF: 0.00548

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.00443

Gnomad4 NFE AF: 0.00435

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00410 Hom.: 0

Bravo AF: 0.00299

Asia WGS AF: 0.00115 AC: 4 AN: 3478

EpiCase AF: 0.00306

EpiControl AF: 0.00326

ClinVar

Significance: Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	COL12A1: BP4, BS2 -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 09, 2020	- -

Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Aug 31, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	23
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.050		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

Other links and lift over

dbSNP: rs181257320; hg19: chr6-75861578;