rs7807121

Variant names:

• chr7-7513909-G-A
• rs7807121
• NM_001037763.3:c.882+1905C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037763.3(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 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.882+1905C>T		intron_variant	Intron 8 of 34	ENST00000399429.8	NP_001032852.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.882+1905C>T		intron_variant	Intron 8 of 34	1	NM_001037763.3	ENSP00000382356.3
COL28A1	ENST00000444268.1	n.81+1905C>T		intron_variant	Intron 3 of 22	5		ENSP00000408401.1

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

African (AFR) AF: 0.142 AC: 5916 AN: 41532

American (AMR) AF: 0.134 AC: 2055 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3472

East Asian (EAS) AF: 0.166 AC: 860 AN: 5186

South Asian (SAS) AF: 0.150 AC: 724 AN: 4818

European-Finnish (FIN) AF: 0.104 AC: 1102 AN: 10586

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7726 AN: 68006

Other (OTH) AF: 0.143 AC: 303 AN: 2112

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
PhyloP100		0.62
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7807121; hg19: chr7-7553540;