rs10104973

chr8-120092146-G-A

Variant summary

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

The ENST00000498051.6(COL14A1):c.-134-13437G>A variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,928 control chromosomes in the GnomAD database, including 45,506 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 0.77 (45506 hom., cov: 29)
• Consequence: COL14A1 ENST00000498051.6 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

LOC105375730 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375730	XR_928593.4	n.1422-13437G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL14A1	ENST00000498051.6	c.-134-13437G>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117459 AN: 151810 Hom.: 45497 Cov.: 29

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.774 AC: 117521 AN: 151928 Hom.: 45506 Cov.: 29 AF XY: 0.775 AC XY: 57534 AN XY: 74248

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.774

Alfa AF: 0.775 Hom.: 89271

Bravo AF: 0.779

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10104973; hg19: chr8-121104385;