rs2502562

Variant names:

• chr6-69884522-G-A
• rs2502562
• NM_001858.6:c.91+4864G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001858.6(COL19A1):​c.91+4864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,106 control chromosomes in the GnomAD database, including 882 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 0.10 (882 hom., cov: 32)
• Consequence: COL19A1 NM_001858.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt
COL19A1	NM_001858.6	c.91+4864G>A		intron_variant	Intron 2 of 50	ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5	c.91+4864G>A		intron_variant	Intron 2 of 50	1	NM_001858.6	ENSP00000480474.1
COL19A1	ENST00000476656.1	n.212+4864G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15690 AN: 151990 Hom.: 876 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.103 AC: 15709 AN: 152106 Hom.: 882 Cov.: 32 AF XY: 0.101 AC XY: 7505 AN XY: 74368

African (AFR) AF: 0.110 AC: 4543 AN: 41480

American (AMR) AF: 0.0781 AC: 1194 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5186

South Asian (SAS) AF: 0.0715 AC: 345 AN: 4822

European-Finnish (FIN) AF: 0.0904 AC: 956 AN: 10580

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.113 AC: 7661 AN: 67974

Other (OTH) AF: 0.111 AC: 233 AN: 2108

Alfa AF: 0.110 Hom.: 1663

Bravo AF: 0.103

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.36
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2502562; hg19: chr6-70594414;