chr6-75086648-G-GTATATA

Position:

• chr6-75086648-G-GTATATA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS1

The NM_004370.6(COL12A1):​c.9182-92_9182-91insTATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 288,980 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0052 (1 hom., cov: 0)
  • Exomes 𝑓: 0.00021 (0 hom.)
• Consequence: COL12A1 NM_004370.6 intron
• Clinical Significance: Likely 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 6-75086648-G-GTATATA is Benign according to our data. Variant chr6-75086648-G-GTATATA is described in ClinVar as [Likely_benign]. Clinvar id is 1211533.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00519 (735/141654) while in subpopulation AFR AF= 0.0164 (633/38666). AF 95% confidence interval is 0.0153. There are 1 homozygotes in gnomad4. There are 354 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00517 AC: 733 AN: 141658 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00276

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00102

Gnomad SAS AF: 0.00136

Gnomad FIN AF: 0.000124

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000677

Gnomad OTH AF: 0.00364

GnomAD4 exome AF: 0.000210 AC: 31 AN: 147326 Hom.: 0 AF XY: 0.000207 AC XY: 17 AN XY: 82126

Gnomad4 AFR exome AF: 0.00118

Gnomad4 AMR exome AF: 0.000464

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000780

Gnomad4 FIN exome AF: 0.000104

Gnomad4 NFE exome AF: 0.000202

Gnomad4 OTH exome AF: 0.000613

GnomAD4 genome AF: 0.00519 AC: 735 AN: 141654 Hom.: 1 Cov.: 0 AF XY: 0.00516 AC XY: 354 AN XY: 68582

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.00275

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00103

Gnomad4 SAS AF: 0.00136

Gnomad4 FIN AF: 0.000124

Gnomad4 NFE AF: 0.000677

Gnomad4 OTH AF: 0.00363

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 15, 2019

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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;