Variant 6-69879738-G-C 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.171G>C(p.Leu57Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,258,860 control chromosomes in the GnomAD database, including 24,646 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.17 ( 2392 hom., cov: 32)

Exomes 𝑓: 0.20 ( 22254 hom. )

Consequence

COL19A1
ENST00000478620.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00700

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 (MetaRNN=0.0014814734).

BP6

Variant 6-69879738-G-C is Benign according to our data. Variant chr6-69879738-G-C is described in ClinVar as [Benign]. Clinvar id is 1232931.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+80G>C		intron_variant		ENST00000620364.5	NP_001849.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
COL19A1	ENST00000478620.2 linkuse as main transcript	c.171G>C	p.Leu57Phe	missense_variant	2/2	1		ENSP00000479481
COL19A1	ENST00000620364.5 linkuse as main transcript	c.91+80G>C		intron_variant		1	NM_001858.6	ENSP00000480474	P1
COL19A1	ENST00000476656.1 linkuse as main transcript	n.212+80G>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25802

AN:

151988

Hom.:

2381

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.227

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:

0.198

AC:

218654

AN:

1106754

Hom.:

22254

Cov.:

AF XY:

0.198

AC XY:

110998

AN XY:

560828

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.113

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.237

Gnomad4 FIN exome

AF:

0.189

Gnomad4 NFE exome

AF:

0.197

Gnomad4 OTH exome

AF:

0.190

GnomAD4 genome

AF:

0.170

AC:

25835

AN:

152106

Hom.:

2392

Cov.:

AF XY:

0.172

AC XY:

12826

AN XY:

74354

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:

0.173

Hom.:

315

Bravo

AF:

0.170

TwinsUK

AF:

0.199

AC:

737

ALSPAC

AF:

0.198

AC:

762

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_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.80

FATHMM_MKL

Benign

0.27

LIST_S2

Benign

0.24

MetaRNN

Benign

0.0015

MutationTaster

Benign

1.0

Vest4

0.11

MVP

0.62

GERP RS

0.82

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