6-69930005-A-T

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.666+305A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,042 control chromosomes in the GnomAD database, including 8,625 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (8625 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0680

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=-0.83).
• BP6: Variant 6-69930005-A-T is Benign according to our data. Variant chr6-69930005-A-T is described in ClinVar as [Benign]. Clinvar id is 1257344.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.666+305A>T		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.666+305A>T		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46123 AN: 151924 Hom.: 8586 Cov.: 32

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.304 AC: 46232 AN: 152042 Hom.: 8625 Cov.: 32 AF XY: 0.303 AC XY: 22539 AN XY: 74320

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.296

Alfa AF: 0.130 Hom.: 230

Bravo AF: 0.316

Asia WGS AF: 0.320 AC: 1099 AN: 3444

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	-0.83
Cadd	Benign	0.81
Dann	Benign	0.40

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: rs6455352; hg19: chr6-70639897;