rs3806052

Positions:

• chr6-70176892-A-C
• chr6-70176892-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001858.6(COL19A1):​c.2667+328A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,052 control chromosomes in the GnomAD database, including 14,297 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14297 hom., cov: 33)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.2667+328A>C		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.2667+328A>C		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65368 AN: 151934 Hom.: 14266 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.452

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.430 AC: 65448 AN: 152052 Hom.: 14297 Cov.: 33 AF XY: 0.425 AC XY: 31570 AN XY: 74332

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.454

Alfa AF: 0.423 Hom.: 2351

Bravo AF: 0.425

Asia WGS AF: 0.383 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	18
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs3806052; hg19: chr6-70886784;