rs7742508

Positions:

• chr6-70067458-G-A

Variant summary

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

The NM_001858.6(COL19A1):​c.1171-965G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,104 control chromosomes in the GnomAD database, including 1,505 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 (1505 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594

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 (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.1171-965G>A		intron_variant		ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.1171-965G>A		intron_variant		1	NM_001858.6	ENSP00000480474	P1

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18329 AN: 151986 Hom.: 1502 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.121 AC: 18342 AN: 152104 Hom.: 1505 Cov.: 32 AF XY: 0.122 AC XY: 9085 AN XY: 74360

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0820 Hom.: 481

Bravo AF: 0.126

Asia WGS AF: 0.204 AC: 706 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	4.2
DANN	Benign	0.37

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: rs7742508; hg19: chr6-70777350;