6-75086648-GTA-G

Position:

• chr6-75086648-GTA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004370.6(COL12A1):​c.9182-93_9182-92del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 288,450 control chromosomes in the GnomAD database, including 30,511 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.61 (28524 hom., cov: 0)
  • Exomes 𝑓: 0.31 (1987 hom.)
• Consequence: COL12A1 NM_004370.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 -10 ACMG points.

• BP6: Variant 6-75086648-GTA-G is Benign according to our data. Variant chr6-75086648-GTA-G is described in ClinVar as [Benign]. Clinvar id is 1252836.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL12A1	NM_004370.6	c.9182-93_9182-92del		intron_variant		ENST00000322507.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL12A1	ENST00000322507.13	c.9182-93_9182-92del		intron_variant		1	NM_004370.6	P4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 87065 AN: 141572 Hom.: 28529 Cov.: 0

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.670

GnomAD4 exome AF: 0.315 AC: 46235 AN: 146882 Hom.: 1987 AF XY: 0.313 AC XY: 25592 AN XY: 81878

Gnomad4 AFR exome AF: 0.143

Gnomad4 AMR exome AF: 0.154

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.256

Gnomad4 SAS exome AF: 0.162

Gnomad4 FIN exome AF: 0.397

Gnomad4 NFE exome AF: 0.341

Gnomad4 OTH exome AF: 0.288

GnomAD4 genome AF: 0.615 AC: 87056 AN: 141568 Hom.: 28524 Cov.: 0 AF XY: 0.615 AC XY: 42142 AN XY: 68530

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.669

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 08, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs61611291; hg19: chr6-75796364;