Genetic Variant COL12A1:c.9182-95_9182-92delTATA (chr6-75086648-GTATA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004370.6(COL12A1):c.9182-95_9182-92delTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0696 in 283,588 control chromosomes in the GnomAD database, including 9 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0070 ( 6 hom., cov: 0)

Exomes 𝑓: 0.13 ( 3 hom. )

Consequence

COL12A1
NM_004370.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL12A1	NM_004370.6 link	c.9182-95_9182-92delTATA		intron_variant	Intron 65 of 65	ENST00000322507.13	NP_004361.3	Q99715-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL12A1	ENST00000322507.13 link	c.9182-95_9182-92delTATA		intron_variant	Intron 65 of 65	1	NM_004370.6	ENSP00000325146.8		Q99715-1

Frequencies

GnomAD3 genomes

AF:

0.00698

AC:

987

AN:

141332

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00795

Gnomad AMI

AF:

0.0134

Gnomad AMR

AF:

0.00602

Gnomad ASJ

AF:

0.00416

Gnomad EAS

AF:

0.00287

Gnomad SAS

AF:

0.0133

Gnomad FIN

AF:

0.00874

Gnomad MID

AF:

0.00699

Gnomad NFE

AF:

0.00628

Gnomad OTH

AF:

0.00886

GnomAD4 exome

AF:

0.132

AC:

18754

AN:

142262

Hom.:

AF XY:

0.133

AC XY:

10544

AN XY:

79306

show subpopulations

Gnomad4 AFR exome

AF:

0.0392

Gnomad4 AMR exome

AF:

0.0697

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.120

Gnomad4 SAS exome

AF:

0.0774

Gnomad4 FIN exome

AF:

0.154

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.00701

AC:

991

AN:

141326

Hom.:

Cov.:

AF XY:

0.00714

AC XY:

488

AN XY:

68382

show subpopulations

Gnomad4 AFR

AF:

0.00804

Gnomad4 AMR

AF:

0.00601

Gnomad4 ASJ

AF:

0.00416

Gnomad4 EAS

AF:

0.00288

Gnomad4 SAS

AF:

0.0134

Gnomad4 FIN

AF:

0.00874

Gnomad4 NFE

AF:

0.00628

Gnomad4 OTH

AF:

0.00883

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

6-75086648-GTATATATATATATA-GTATATATATA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over