6-75086648-G-GTATATA

Variant names:

• chr6-75086648-G-GTATATA
• rs61611291
• NM_004370.6:c.9182-97_9182-92dupTATATA

Variant summary

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

The NM_004370.6(COL12A1):​c.9182-97_9182-92dupTATATA 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 rank	MANE	Protein	UniProt
COL12A1	NM_004370.6	c.9182-97_9182-92dupTATATA		intron_variant	Intron 65 of 65	ENST00000322507.13	NP_004361.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL12A1	ENST00000322507.13	c.9182-92_9182-91insTATATA		intron_variant	Intron 65 of 65	1	NM_004370.6	ENSP00000325146.8

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

Sep 15, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;