6-69879819-T-A

Variant summary

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

The ENST00000478620.2(COL19A1):c.*69T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 663,968 control chromosomes in the GnomAD database, including 12,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2403 hom., cov: 33)
  • Exomes 𝑓: 0.19 (9615 hom.)
• Consequence: COL19A1 ENST00000478620.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.591

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=-0.82).
• BP6: Variant 6-69879819-T-A is Benign according to our data. Variant chr6-69879819-T-A is described in ClinVar as [Benign]. Clinvar id is 1232646.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.91+161T>A		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000478620.2	c.*69T>A		3_prime_UTR_variant	2/2	1
COL19A1	ENST00000620364.5	c.91+161T>A		intron_variant		1	NM_001858.6	P1
COL19A1	ENST00000476656.1	n.212+161T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25813 AN: 152086 Hom.: 2392 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.173

GnomAD4 exome AF: 0.187 AC: 95734 AN: 511764 Hom.: 9615 Cov.: 7 AF XY: 0.188 AC XY: 49920 AN XY: 265252

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.238

Gnomad4 SAS exome AF: 0.233

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.179

GnomAD4 genome AF: 0.170 AC: 25846 AN: 152204 Hom.: 2403 Cov.: 33 AF XY: 0.173 AC XY: 12845 AN XY: 74420

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.182

Alfa AF: 0.0833 Hom.: 135

Bravo AF: 0.170

Asia WGS AF: 0.261 AC: 907 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.5
Dann	Benign	0.32

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: rs13194248; hg19: chr6-70589711;