rs10945200

Variant names:

• chr6-70181848-G-A
• rs10945200
• NM_001858.6:c.2775+1325G>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.2775+1325G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,892 control chromosomes in the GnomAD database, including 13,804 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 0.42 (13804 hom., cov: 31)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.2775+1325G>A		intron_variant	Intron 44 of 50	ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.2775+1325G>A		intron_variant	Intron 44 of 50	1	NM_001858.6	ENSP00000480474.1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64200 AN: 151772 Hom.: 13773 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.423 AC: 64283 AN: 151892 Hom.: 13804 Cov.: 31 AF XY: 0.418 AC XY: 31021 AN XY: 74226

African (AFR) AF: 0.403 AC: 16690 AN: 41400

American (AMR) AF: 0.376 AC: 5747 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2004 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5144

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4816

European-Finnish (FIN) AF: 0.385 AC: 4059 AN: 10542

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30639 AN: 67942

Other (OTH) AF: 0.449 AC: 947 AN: 2110

Alfa AF: 0.442 Hom.: 64402

Bravo AF: 0.417

Asia WGS AF: 0.381 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.039
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10945200; hg19: chr6-70891740;