6-75086648-G-GTATA

Position:

• chr6-75086648-G-GTATA

Variant summary

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

The NM_004370.6(COL12A1):​c.9182-92_9182-91insTATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 288,876 control chromosomes in the GnomAD database, including 101 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.023 (101 hom., cov: 0)
  • Exomes 𝑓: 0.00096 (0 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-G-GTATA is Benign according to our data. Variant chr6-75086648-G-GTATA is described in ClinVar as [Benign]. Clinvar id is 1228153.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL12A1	NM_004370.6	c.9182-92_9182-91insTATA		intron_variant		ENST00000322507.13	NP_004361.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL12A1	ENST00000322507.13	c.9182-92_9182-91insTATA		intron_variant		1	NM_004370.6	ENSP00000325146	P4

Frequencies

GnomAD3 genomes AF: 0.0233 AC: 3296 AN: 141596 Hom.: 99 Cov.: 0

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0125

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.00181

Gnomad FIN AF: 0.000124

Gnomad MID AF: 0.00694

Gnomad NFE AF: 0.00165

Gnomad OTH AF: 0.0182

GnomAD4 exome AF: 0.000957 AC: 141 AN: 147286 Hom.: 0 AF XY: 0.000974 AC XY: 80 AN XY: 82110

Gnomad4 AFR exome AF: 0.0106

Gnomad4 AMR exome AF: 0.00155

Gnomad4 ASJ exome AF: 0.000234

Gnomad4 EAS exome AF: 0.000868

Gnomad4 SAS exome AF: 0.00101

Gnomad4 FIN exome AF: 0.000208

Gnomad4 NFE exome AF: 0.000763

Gnomad4 OTH exome AF: 0.00199

GnomAD4 genome AF: 0.0233 AC: 3303 AN: 141590 Hom.: 101 Cov.: 0 AF XY: 0.0236 AC XY: 1617 AN XY: 68548

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.0125

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0125

Gnomad4 SAS AF: 0.00182

Gnomad4 FIN AF: 0.000124

Gnomad4 NFE AF: 0.00165

Gnomad4 OTH AF: 0.0192

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 30, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;