Variant 6-69932768-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001858.6(COL19A1):c.667-15C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,514,458 control chromosomes in the GnomAD database, including 11,236 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.11 ( 978 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10258 hom. )

Consequence

COL19A1
NM_001858.6 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.504

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 6-69932768-C-T is Benign according to our data. Variant chr6-69932768-C-T is described in ClinVar as [Benign]. Clinvar id is 1174254.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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.667-15C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL19A1	ENST00000620364.5 linkuse as main transcript	c.667-15C>T		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001858.6	ENSP00000480474	P1

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16349

AN:

151930

Hom.:

977

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0956

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.0921

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0959

Gnomad FIN

AF:

0.0831

Gnomad MID

AF:

0.155

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.125

GnomAD3 exomes

AF:

0.101

AC:

22983

AN:

227790

Hom.:

1448

AF XY:

0.104

AC XY:

12840

AN XY:

123658

show subpopulations

Gnomad AFR exome

AF:

0.0909

Gnomad AMR exome

AF:

0.0670

Gnomad ASJ exome

AF:

0.204

Gnomad EAS exome

AF:

0.000476

Gnomad SAS exome

AF:

0.0990

Gnomad FIN exome

AF:

0.0816

Gnomad NFE exome

AF:

0.123

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.117

AC:

159333

AN:

1362410

Hom.:

10258

Cov.:

AF XY:

0.117

AC XY:

79618

AN XY:

681488

show subpopulations

Gnomad4 AFR exome

AF:

0.0953

Gnomad4 AMR exome

AF:

0.0718

Gnomad4 ASJ exome

AF:

0.200

Gnomad4 EAS exome

AF:

0.000472

Gnomad4 SAS exome

AF:

0.100

Gnomad4 FIN exome

AF:

0.0837

Gnomad4 NFE exome

AF:

0.124

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.108

AC:

16367

AN:

152048

Hom.:

978

Cov.:

AF XY:

0.104

AC XY:

7718

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0958

Gnomad4 AMR

AF:

0.0919

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0953

Gnomad4 FIN

AF:

0.0831

Gnomad4 NFE

AF:

0.125

Gnomad4 OTH

AF:

0.124

Alfa

AF:

0.124

Hom.:

269

Bravo

AF:

0.108

Asia WGS

AF:

0.0450

AC:

158

AN:

3476

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

6.6

DANN

Benign

0.39

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