6-69879831-A-G

Variant summary

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

The ENST00000478620.2(COL19A1):c.*81A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 621,942 control chromosomes in the GnomAD database, including 3,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (891 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2676 hom.)
• Consequence: COL19A1 ENST00000478620.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.533

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=-0.85).
• BP6: Variant 6-69879831-A-G is Benign according to our data. Variant chr6-69879831-A-G is described in ClinVar as [Benign]. Clinvar id is 1272189.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.91+173A>G		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000478620.2	c.*81A>G		3_prime_UTR_variant	2/2	1
COL19A1	ENST00000620364.5	c.91+173A>G		intron_variant		1	NM_001858.6	P1
COL19A1	ENST00000476656.1	n.212+173A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15708 AN: 152138 Hom.: 884 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0909

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.112

GnomAD4 exome AF: 0.0998 AC: 46873 AN: 469684 Hom.: 2676 Cov.: 6 AF XY: 0.0993 AC XY: 24272 AN XY: 244342

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.0729

Gnomad4 ASJ exome AF: 0.180

Gnomad4 EAS exome AF: 0.000194

Gnomad4 SAS exome AF: 0.0764

Gnomad4 FIN exome AF: 0.0869

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.103 AC: 15730 AN: 152258 Hom.: 891 Cov.: 32 AF XY: 0.101 AC XY: 7521 AN XY: 74468

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0781

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0713

Gnomad4 FIN AF: 0.0909

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.110

Alfa AF: 0.110 Hom.: 135

Bravo AF: 0.103

Asia WGS AF: 0.0400 AC: 137 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	-0.85
Cadd	Benign	6.5
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: rs2487439; hg19: chr6-70589723;