Variant 6-69879831-A-G 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.*81A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 621,942 control chromosomes in the GnomAD database, including 3,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 891 hom., cov: 32)

Exomes 𝑓: 0.10 ( 2676 hom. )

Consequence

COL19A1
ENST00000478620.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.533

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=-0.85).

BP6

Variant 6-69879831-A-G is Benign according to our data. Variant chr6-69879831-A-G is described in ClinVar as [Benign]. Clinvar id is 1272189.Status of the report is criteria_provided_single_submitter, 1 stars.

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/exons	MANE	Protein	UniProt
COL19A1	NM_001858.6 linkuse as main transcript	c.91+173A>G		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.*81A>G	3_prime_UTR_variant	2/2	1		ENSP00000479481
COL19A1	ENST00000620364.5 linkuse as main transcript	c.91+173A>G	intron_variant		1	NM_001858.6	ENSP00000480474	P1
COL19A1	ENST00000476656.1 linkuse as main transcript	n.212+173A>G	intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15708

AN:

152138

Hom.:

884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.109

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.0782

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0718

Gnomad FIN

AF:

0.0909

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.113

Gnomad OTH

AF:

0.112

GnomAD4 exome

AF:

0.0998

AC:

46873

AN:

469684

Hom.:

2676

Cov.:

AF XY:

0.0993

AC XY:

24272

AN XY:

244342

show subpopulations

Gnomad4 AFR exome

AF:

0.110

Gnomad4 AMR exome

AF:

0.0729

Gnomad4 ASJ exome

AF:

0.180

Gnomad4 EAS exome

AF:

0.000194

Gnomad4 SAS exome

AF:

0.0764

Gnomad4 FIN exome

AF:

0.0869

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.103

AC:

15730

AN:

152258

Hom.:

891

Cov.:

AF XY:

0.101

AC XY:

7521

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.109

Gnomad4 AMR

AF:

0.0781

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.000964

Gnomad4 SAS

AF:

0.0713

Gnomad4 FIN

AF:

0.0909

Gnomad4 NFE

AF:

0.113

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.110

Hom.:

135

Bravo

AF:

0.103

Asia WGS

AF:

0.0400

AC:

137

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

-0.85

CADD

Benign

6.5

DANN

Benign

0.56

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