8-120147628-C-T

Position:

• chr8-120147628-C-T

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.-37-178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 152,226 control chromosomes in the GnomAD database, including 52,500 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.83 (52500 hom., cov: 33)
• Consequence: COL14A1 NM_021110.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0620

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=-0.9).
• BP6: Variant 8-120147628-C-T is Benign according to our data. Variant chr8-120147628-C-T is described in ClinVar as [Benign]. Clinvar id is 1221897.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL14A1	NM_021110.4	c.-37-178C>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.-37-178C>T		intron_variant		5	NM_021110.4	ENSP00000297848.3

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125724 AN: 152108 Hom.: 52449 Cov.: 33

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.827 AC: 125829 AN: 152226 Hom.: 52500 Cov.: 33 AF XY: 0.826 AC XY: 61488 AN XY: 74408

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.810

Alfa AF: 0.802 Hom.: 6133

Bravo AF: 0.839

Asia WGS AF: 0.704 AC: 2451 AN: 3478

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 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.56

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: rs6995843; hg19: chr8-121159867;