rs7807121

Positions:

• chr7-7513909-G-A

Variant summary

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

The ENST00000399429.8(COL28A1):​c.882+1905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,208 control chromosomes in the GnomAD database, including 1,275 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 0.13 (1275 hom., cov: 32)
• Consequence: COL28A1 ENST00000399429.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

Genes affected

COL28A1 (HGNC:22442): (collagen type XXVIII alpha 1 chain) COL28A1 belongs to a class of collagens containing von Willebrand factor (VWF; MIM 613160) type A (VWFA) domains (Veit et al., 2006 [PubMed 16330543]).[supplied by OMIM, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.882+1905C>T		intron_variant		ENST00000399429.8	NP_001032852.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.882+1905C>T		intron_variant		1	NM_001037763.3	ENSP00000382356	P1
COL28A1	ENST00000444268.1	c.81+1905C>T		intron_variant, NMD_transcript_variant		5		ENSP00000408401

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19185 AN: 152090 Hom.: 1272 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.126 AC: 19200 AN: 152208 Hom.: 1275 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74404

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.143

Alfa AF: 0.121 Hom.: 168

Bravo AF: 0.129

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.63

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: rs7807121; hg19: chr7-7553540;