chr8-120168428-C-T

Position:

• chr8-120168428-C-T

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+181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,962 control chromosomes in the GnomAD database, including 9,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.33 (9242 hom., cov: 32)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.518

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=-0.96).
• BP6: Variant 8-120168428-C-T is Benign according to our data. Variant chr8-120168428-C-T is described in ClinVar as [Benign]. Clinvar id is 1267450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4	c.436+181C>T		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+181C>T		intron_variant		5	NM_021110.4	ENSP00000297848.3

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50756 AN: 151844 Hom.: 9242 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.334 AC: 50758 AN: 151962 Hom.: 9242 Cov.: 32 AF XY: 0.335 AC XY: 24845 AN XY: 74250

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.378

Alfa AF: 0.370 Hom.: 19887

Bravo AF: 0.345

Asia WGS AF: 0.296 AC: 1028 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	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	-0.96
CADD	Benign	0.37
DANN	Benign	0.69

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: rs2198751; hg19: chr8-121180667; COSMIC: COSV52849920;