chr6-70084316-C-T

Variant names:

• chr6-70084316-C-T
• rs1983761
• NM_001858.6:c.1224+15840C>T

Variant summary

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

The NM_001858.6(COL19A1):​c.1224+15840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,120 control chromosomes in the GnomAD database, including 452 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 0.064 (452 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.1224+15840C>T		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+15840C>T		intron_variant	Intron 15 of 50	1	NM_001858.6	ENSP00000480474.1

Frequencies

GnomAD3 genomes AF: 0.0642 AC: 9754 AN: 152002 Hom.: 452 Cov.: 32

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0641 AC: 9750 AN: 152120 Hom.: 452 Cov.: 32 AF XY: 0.0622 AC XY: 4621 AN XY: 74352

Gnomad4 AFR AF: 0.0171

Gnomad4 AMR AF: 0.0587

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0512

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0965

Gnomad4 OTH AF: 0.0767

Alfa AF: 0.0865 Hom.: 284

Bravo AF: 0.0592

Asia WGS AF: 0.0240 AC: 82 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	2.1
DANN	Benign	0.56

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: rs1983761; hg19: chr6-70794208;