6-69929155-TAC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001858.6(COL19A1):c.391-245_391-244del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.13 (1291 hom., cov: 0)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.400

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 -10 ACMG points.

• BP6: Variant 6-69929155-TAC-T is Benign according to our data. Variant chr6-69929155-TAC-T is described in ClinVar as [Benign]. Clinvar id is 1271148.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.391-245_391-244del		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.391-245_391-244del		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 18747 AN: 148286 Hom.: 1291 Cov.: 0

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0787

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.00256

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.126 AC: 18759 AN: 148388 Hom.: 1291 Cov.: 0 AF XY: 0.122 AC XY: 8788 AN XY: 72324

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.00257

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.137

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 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs141935825; hg19: chr6-70639047;