6-69899263-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001858.6(COL19A1):c.166+241C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 150,978 control chromosomes in the GnomAD database, including 2,247 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (2247 hom., cov: 30)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.234

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 6-69899263-C-G is Benign according to our data. Variant chr6-69899263-C-G is described in ClinVar as [Benign]. Clinvar id is 1237942.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.166+241C>G		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.166+241C>G		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23347 AN: 150868 Hom.: 2245 Cov.: 30

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.0955

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.155 AC: 23380 AN: 150978 Hom.: 2247 Cov.: 30 AF XY: 0.150 AC XY: 11060 AN XY: 73682

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.158

Alfa AF: 0.0491 Hom.: 45

Bravo AF: 0.162

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.49

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: rs10428870; hg19: chr6-70609155;