rs3806005

Variant names:

• chr6-70074009-C-A
• rs3806005
• NM_001858.6:c.1224+5533C>A

Variant summary

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

The NM_001858.6(COL19A1):​c.1224+5533C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,178 control chromosomes in the GnomAD database, including 1,196 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 0.12 (1196 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 1 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.1224+5533C>A		intron_variant	Intron 15 of 50	ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.1224+5533C>A		intron_variant	Intron 15 of 50	1	NM_001858.6	ENSP00000480474.1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17592 AN: 152060 Hom.: 1188 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.116 AC: 17620 AN: 152178 Hom.: 1196 Cov.: 32 AF XY: 0.119 AC XY: 8853 AN XY: 74388

African (AFR) AF: 0.150 AC: 6239 AN: 41522

American (AMR) AF: 0.201 AC: 3066 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3470

East Asian (EAS) AF: 0.0660 AC: 341 AN: 5168

South Asian (SAS) AF: 0.181 AC: 872 AN: 4826

European-Finnish (FIN) AF: 0.0822 AC: 870 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0785 AC: 5341 AN: 68010

Other (OTH) AF: 0.132 AC: 280 AN: 2116

Alfa AF: 0.0935 Hom.: 147

Bravo AF: 0.124

Asia WGS AF: 0.147 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.3
DANN	Benign	0.75
PhyloP100		-0.053
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: rs3806005; hg19: chr6-70783901;