rs6469916

chr8-120320552-G-Achr8-120320552-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021110.4(COL14A1):c.4659+4555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,236 control chromosomes in the GnomAD database, including 64,687 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.92 (64687 hom., cov: 32)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL14A1	NM_021110.4	c.4659+4555G>A		intron_variant		ENST00000297848.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL14A1	ENST00000297848.8	c.4659+4555G>A		intron_variant		5	NM_021110.4	A1
COL14A1	ENST00000309791.8	c.4659+4555G>A		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140088 AN: 152118 Hom.: 64633 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.921 AC: 140203 AN: 152236 Hom.: 64687 Cov.: 32 AF XY: 0.924 AC XY: 68794 AN XY: 74436

Gnomad4 AFR AF: 0.964

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.912

Alfa AF: 0.892 Hom.: 37381

Bravo AF: 0.920

Asia WGS AF: 0.943 AC: 3274 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	10
Dann	Benign	0.57

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: rs6469916; hg19: chr8-121332791;