rs3793039

Variant names:

• chr6-70031317-A-G
• rs3793039
• NM_001858.6:c.1081-2928A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001858.6(COL19A1):​c.1081-2928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,656 control chromosomes in the GnomAD database, including 7,906 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 0.30 (7906 hom., cov: 31)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.1081-2928A>G		intron_variant	Intron 12 of 50	ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.1081-2928A>G		intron_variant	Intron 12 of 50	1	NM_001858.6	ENSP00000480474.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45991 AN: 151536 Hom.: 7889 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.304 AC: 46050 AN: 151656 Hom.: 7906 Cov.: 31 AF XY: 0.300 AC XY: 22192 AN XY: 74054

African (AFR) AF: 0.457 AC: 18874 AN: 41322

American (AMR) AF: 0.242 AC: 3689 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3466

East Asian (EAS) AF: 0.0809 AC: 417 AN: 5156

South Asian (SAS) AF: 0.200 AC: 958 AN: 4794

European-Finnish (FIN) AF: 0.214 AC: 2246 AN: 10486

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.257 AC: 17467 AN: 67910

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.272 Hom.: 9885

Bravo AF: 0.315

Asia WGS AF: 0.160 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.66
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3793039; hg19: chr6-70741209;