6-69929155-T-TACACACACAC

Variant summary

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

The NM_001858.6(COL19A1):c.391-253_391-244dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.077 (509 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-T-TACACACACAC is Benign according to our data. Variant chr6-69929155-T-TACACACACAC is described in ClinVar as [Benign]. Clinvar id is 1179345.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.391-253_391-244dup		intron_variant		ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.391-253_391-244dup		intron_variant		1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11347 AN: 148450 Hom.: 510 Cov.: 0

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00899

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0355

Gnomad EAS AF: 0.0755

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0765 AC: 11366 AN: 148552 Hom.: 509 Cov.: 0 AF XY: 0.0782 AC XY: 5664 AN XY: 72416

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0355

Gnomad4 EAS AF: 0.0758

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0552

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0727

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

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Computational scores

Source: dbNSFP v4.3

Splicing

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;