Variant 8-120196761-A-C 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.437-30A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 1,605,426 control chromosomes in the GnomAD database, including 58,110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7352 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50758 hom. )

Consequence

COL14A1
NM_021110.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.49

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=-0.84).

BP6

Variant 8-120196761-A-C is Benign according to our data. Variant chr8-120196761-A-C is described in ClinVar as [Benign]. Clinvar id is 1268056.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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.437-30A>C		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.437-30A>C		intron_variant		5	NM_021110.4	ENSP00000297848.3		Q05707-1

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45459

AN:

151990

Hom.:

7345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.170

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.252

GnomAD3 exomes

AF:

0.261

AC:

64334

AN:

246252

Hom.:

8974

AF XY:

0.262

AC XY:

34837

AN XY:

133150

show subpopulations

Gnomad AFR exome

AF:

0.431

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.251

Gnomad EAS exome

AF:

0.154

Gnomad SAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.260

Gnomad NFE exome

AF:

0.256

Gnomad OTH exome

AF:

0.256

GnomAD4 exome

AF:

0.260

AC:

377260

AN:

1453318

Hom.:

50758

Cov.:

AF XY:

0.261

AC XY:

188411

AN XY:

722656

show subpopulations

Gnomad4 AFR exome

AF:

0.434

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.251

Gnomad4 EAS exome

AF:

0.184

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.257

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.299

AC:

45490

AN:

152108

Hom.:

7352

Cov.:

AF XY:

0.297

AC XY:

22110

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.424

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.169

Gnomad4 SAS

AF:

0.310

Gnomad4 FIN

AF:

0.272

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.252

Alfa

AF:

0.264

Hom.:

9674

Bravo

AF:

0.300

Asia WGS

AF:

0.262

AC:

914

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.84

CADD

Benign

0.58

DANN

Benign

0.45

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