6-69899165-A-AT

Position:

• chr6-69899165-A-AT

Variant summary

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

The NM_001858.6(COL19A1):​c.166+160dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 423,964 control chromosomes in the GnomAD database, including 1,057 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.11 (979 hom., cov: 29)
  • Exomes 𝑓: 0.16 (78 hom.)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.177

Genes affected

COL19A1 (HGNC:2196): (collagen type XIX alpha 1 chain) This gene encodes the alpha chain of type XIX collagen, a member of the FACIT collagen family (fibril-associated collagens with interrupted helices). Although the function of this collagen is not known, other members of this collagen family are found in association with fibril-forming collagens such as type I and II, and serve to maintain the integrity of the extracellular matrix. The transcript produced from this gene has an unusually large 3' UTR which has not been completely sequenced. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-69899165-A-AT is Benign according to our data. Variant chr6-69899165-A-AT is described in ClinVar as [Benign]. Clinvar id is 1295067.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.166+160dup		intron_variant		ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.166+160dup		intron_variant		1	NM_001858.6	ENSP00000480474	P1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 15667 AN: 140654 Hom.: 979 Cov.: 29

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.0596

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0161

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0679

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.157 AC: 44585 AN: 283308 Hom.: 78 AF XY: 0.159 AC XY: 24101 AN XY: 151742

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.144

Gnomad4 ASJ exome AF: 0.206

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.163

GnomAD4 genome AF: 0.111 AC: 15668 AN: 140656 Hom.: 979 Cov.: 29 AF XY: 0.107 AC XY: 7254 AN XY: 68080

Gnomad4 AFR AF: 0.0987

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.0679

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.130

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

Jun 19, 2021

- -

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: rs112888229; hg19: chr6-70609057;