rs9446187

chr6-70076574-G-A

Variant summary

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

The NM_001858.6(COL19A1):c.1224+8098G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,120 control chromosomes in the GnomAD database, including 4,005 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 0.19 (4005 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.1224+8098G>A		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.1224+8098G>A		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29029 AN: 152004 Hom.: 3989 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.191 AC: 29075 AN: 152120 Hom.: 4005 Cov.: 32 AF XY: 0.195 AC XY: 14540 AN XY: 74386

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0826

Gnomad4 NFE AF: 0.0806

Gnomad4 OTH AF: 0.193

Alfa AF: 0.123 Hom.: 517

Bravo AF: 0.205

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.40
Dann	Benign	0.54

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: rs9446187; hg19: chr6-70786466;