6-70074854-G-T

Variant names:

• chr6-70074854-G-T
• rs3793048
• NM_001858.6:c.1224+6378G>T

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+6378G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,074 control chromosomes in the GnomAD database, including 7,948 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 0.25 (7948 hom., cov: 33)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001858.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL19A1	NM_001858.6	MANE Select	c.1224+6378G>T		intron	N/A	NP_001849.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL19A1	ENST00000620364.5	TSL:1 MANE Select	c.1224+6378G>T		intron	N/A	ENSP00000480474.1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37720 AN: 151956 Hom.: 7911 Cov.: 33

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.249 AC: 37820 AN: 152074 Hom.: 7948 Cov.: 33 AF XY: 0.250 AC XY: 18571 AN XY: 74328

African (AFR) AF: 0.560 AC: 23219 AN: 41454

American (AMR) AF: 0.277 AC: 4231 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1432 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4826

European-Finnish (FIN) AF: 0.0824 AC: 872 AN: 10578

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5519 AN: 67986

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.132 Hom.: 7789

Bravo AF: 0.271

Asia WGS AF: 0.346 AC: 1201 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.61
PhyloP100		-0.40
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: rs3793048; hg19: chr6-70784746;