6-70210909-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001858.6(COL19A1):c.*3635T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,138 control chromosomes in the GnomAD database, including 52,851 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52851 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL19A1	NM_001858.6	c.*3635T>C		3_prime_UTR_variant	51/51	ENST00000620364.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL19A1	ENST00000620364.5	c.*3635T>C		3_prime_UTR_variant	51/51	1	NM_001858.6	P1

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125898 AN: 152020 Hom.: 52781 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.828 AC: 126029 AN: 152138 Hom.: 52851 Cov.: 32 AF XY: 0.827 AC XY: 61514 AN XY: 74370

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.809

Alfa AF: 0.775 Hom.: 60755

Bravo AF: 0.844

Asia WGS AF: 0.856 AC: 2977 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.14
Dann	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs624243; hg19: chr6-70920612;