8-120158564-G-A

Position:

• chr8-120158564-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_021110.4(COL14A1):​c.205+318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,906 control chromosomes in the GnomAD database, including 12,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (12932 hom., cov: 32)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.129

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 8-120158564-G-A is Benign according to our data. Variant chr8-120158564-G-A is described in ClinVar as [Benign]. Clinvar id is 1235618.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4	c.205+318G>A		intron_variant		ENST00000297848.8	NP_066933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL14A1	ENST00000297848.8	c.205+318G>A		intron_variant		5	NM_021110.4	ENSP00000297848.3

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58547 AN: 151788 Hom.: 12926 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.314

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.386 AC: 58603 AN: 151906 Hom.: 12932 Cov.: 32 AF XY: 0.386 AC XY: 28667 AN XY: 74228

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.313

Alfa AF: 0.342 Hom.: 1952

Bravo AF: 0.383

Asia WGS AF: 0.267 AC: 926 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.51

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

Other links and lift over

dbSNP: rs35420329; hg19: chr8-121170803;