Variant 6-69879819-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000478620.2(COL19A1):c.*69T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 663,968 control chromosomes in the GnomAD database, including 12,018 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2403 hom., cov: 33)

Exomes 𝑓: 0.19 ( 9615 hom. )

Consequence

COL19A1
ENST00000478620.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.591

Variant links:

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]

COL19A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 6-69879819-T-A is Benign according to our data. Variant chr6-69879819-T-A is described in ClinVar as [Benign]. Clinvar id is 1232646.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL19A1	NM_001858.6 linkuse as main transcript	c.91+161T>A		intron_variant		ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
COL19A1	ENST00000478620.2 linkuse as main transcript	c.*69T>A	3_prime_UTR_variant	2/2	1		ENSP00000479481
COL19A1	ENST00000620364.5 linkuse as main transcript	c.91+161T>A	intron_variant		1	NM_001858.6	ENSP00000480474	P1
COL19A1	ENST00000476656.1 linkuse as main transcript	n.212+161T>A	intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25813

AN:

152086

Hom.:

2392

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.173

GnomAD4 exome

AF:

0.187

AC:

95734

AN:

511764

Hom.:

9615

Cov.:

AF XY:

0.188

AC XY:

49920

AN XY:

265252

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.230

Gnomad4 ASJ exome

AF:

0.111

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.182

Gnomad4 OTH exome

AF:

0.179

GnomAD4 genome

AF:

0.170

AC:

25846

AN:

152204

Hom.:

2403

Cov.:

AF XY:

0.173

AC XY:

12845

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.227

Gnomad4 ASJ

AF:

0.118

Gnomad4 EAS

AF:

0.245

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.181

Gnomad4 NFE

AF:

0.183

Gnomad4 OTH

AF:

0.182

Alfa

AF:

0.0833

Hom.:

135

Bravo

AF:

0.170

Asia WGS

AF:

0.261

AC:

907

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-0.82

CADD

Benign

1.5

DANN

Benign

0.32

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over