chr8-120168425-G-A

Position:

• chr8-120168425-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_021110.4(COL14A1):​c.436+178G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,942 control chromosomes in the GnomAD database, including 5,364 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.22 (5364 hom., cov: 32)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.345

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 8-120168425-G-A is Benign according to our data. Variant chr8-120168425-G-A is described in ClinVar as [Benign]. Clinvar id is 1224105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4	c.436+178G>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.436+178G>A		intron_variant		5	NM_021110.4	ENSP00000297848.3

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32783 AN: 151824 Hom.: 5347 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.216 AC: 32850 AN: 151942 Hom.: 5364 Cov.: 32 AF XY: 0.214 AC XY: 15884 AN XY: 74278

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.203

Alfa AF: 0.144 Hom.: 478

Bravo AF: 0.231

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	-0.89
CADD	Benign	0.91
DANN	Benign	0.49

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: rs56122736; hg19: chr8-121180664;