Variant 8-120162598-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_021110.4(COL14A1):c.349+29C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0805 in 1,559,966 control chromosomes in the GnomAD database, including 5,797 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.064 ( 425 hom., cov: 33)

Exomes 𝑓: 0.082 ( 5372 hom. )

Consequence

COL14A1
NM_021110.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.280

Variant links:

Genes affected

COL14A1 (HGNC:2191): (collagen type XIV alpha 1 chain) This gene encodes the alpha chain of type XIV collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XIV collagen interacts with the fibril surface and is involved in the regulation of fibrillogenesis. [provided by RefSeq, Jan 2013]

COL14A1 links:

COL14A1 (HGNC:):

COL14A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

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

BP6

Variant 8-120162598-C-G is Benign according to our data. Variant chr8-120162598-C-G is described in ClinVar as [Benign]. Clinvar id is 1252899.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4 linkuse as main transcript	c.349+29C>G		intron_variant		ENST00000297848.8	NP_066933.1	Q05707-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL14A1	ENST00000297848.8 linkuse as main transcript	c.349+29C>G		intron_variant		5	NM_021110.4	ENSP00000297848.3		Q05707-1

Frequencies

GnomAD3 genomes

AF:

0.0638

AC:

9713

AN:

152174

Hom.:

425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0177

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.0654

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0103

Gnomad FIN

AF:

0.0735

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0924

Gnomad OTH

AF:

0.0935

GnomAD3 exomes

AF:

0.0666

AC:

14272

AN:

214204

Hom.:

626

AF XY:

0.0674

AC XY:

7806

AN XY:

115826

show subpopulations

Gnomad AFR exome

AF:

0.0166

Gnomad AMR exome

AF:

0.0609

Gnomad ASJ exome

AF:

0.0826

Gnomad EAS exome

AF:

0.000122

Gnomad SAS exome

AF:

0.0103

Gnomad FIN exome

AF:

0.0747

Gnomad NFE exome

AF:

0.0949

Gnomad OTH exome

AF:

0.0771

GnomAD4 exome

AF:

0.0823

AC:

115803

AN:

1407674

Hom.:

5372

Cov.:

AF XY:

0.0804

AC XY:

56070

AN XY:

697722

show subpopulations

Gnomad4 AFR exome

AF:

0.0140

Gnomad4 AMR exome

AF:

0.0634

Gnomad4 ASJ exome

AF:

0.0744

Gnomad4 EAS exome

AF:

0.0000777

Gnomad4 SAS exome

AF:

0.0102

Gnomad4 FIN exome

AF:

0.0740

Gnomad4 NFE exome

AF:

0.0938

Gnomad4 OTH exome

AF:

0.0758

GnomAD4 genome

AF:

0.0638

AC:

9712

AN:

152292

Hom.:

425

Cov.:

AF XY:

0.0624

AC XY:

4649

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.0177

Gnomad4 AMR

AF:

0.0843

Gnomad4 ASJ

AF:

0.0654

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.0101

Gnomad4 FIN

AF:

0.0735

Gnomad4 NFE

AF:

0.0924

Gnomad4 OTH

AF:

0.0930

Alfa

AF:

0.0485

Hom.:

Bravo

AF:

0.0645

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

DANN

Benign

0.19

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