Variant 6-75086648-G-GTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004370.6(COL12A1):c.9182-92_9182-91insTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 288,312 control chromosomes in the GnomAD database, including 1,321 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 1320 hom., cov: 0)

Exomes 𝑓: 0.018 ( 1 hom. )

Consequence

COL12A1
NM_004370.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 -10 ACMG points.

BP6

Variant 6-75086648-G-GTA is Benign according to our data. Variant chr6-75086648-G-GTA is described in ClinVar as [Benign]. Clinvar id is 1264862.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL12A1	NM_004370.6 linkuse as main transcript	c.9182-92_9182-91insTA		intron_variant		ENST00000322507.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL12A1	ENST00000322507.13 linkuse as main transcript	c.9182-92_9182-91insTA		intron_variant		1	NM_004370.6	P4	Q99715-1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

15063

AN:

141482

Hom.:

1322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.0675

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.0235

Gnomad SAS

AF:

0.0493

Gnomad FIN

AF:

0.0354

Gnomad MID

AF:

0.0590

Gnomad NFE

AF:

0.0524

Gnomad OTH

AF:

0.0796

GnomAD4 exome

AF:

0.0179

AC:

2631

AN:

146836

Hom.:

AF XY:

0.0174

AC XY:

1425

AN XY:

81822

show subpopulations

Gnomad4 AFR exome

AF:

0.0567

Gnomad4 AMR exome

AF:

0.00945

Gnomad4 ASJ exome

AF:

0.0120

Gnomad4 EAS exome

AF:

0.00573

Gnomad4 SAS exome

AF:

0.00921

Gnomad4 FIN exome

AF:

0.0241

Gnomad4 NFE exome

AF:

0.0185

Gnomad4 OTH exome

AF:

0.0172

GnomAD4 genome

AF:

0.106

AC:

15060

AN:

141476

Hom.:

1320

Cov.:

AF XY:

0.104

AC XY:

7118

AN XY:

68500

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.0675

Gnomad4 ASJ

AF:

0.0300

Gnomad4 EAS

AF:

0.0236

Gnomad4 SAS

AF:

0.0489

Gnomad4 FIN

AF:

0.0354

Gnomad4 NFE

AF:

0.0524

Gnomad4 OTH

AF:

0.0793

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over