7-7362323-T-G

Variant names:

• chr7-7362323-T-G
• rs7800159
• NM_001037763.3:c.3067-1795A>C

Variant summary

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

The NM_001037763.3(COL28A1):​c.3067-1795A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 151,976 control chromosomes in the GnomAD database, including 46,431 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 0.78 (46431 hom., cov: 31)
• Consequence: COL28A1 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 2 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]

LOC107986764 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001037763.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL28A1	NM_001037763.3	MANE Select	c.3067-1795A>C		intron	N/A	NP_001032852.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL28A1	ENST00000399429.8	TSL:1 MANE Select	c.3067-1795A>C		intron	N/A	ENSP00000382356.3
	COL28A1	ENST00000430711.5	TSL:5	n.118-1795A>C		intron	N/A	ENSP00000413093.1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118481 AN: 151858 Hom.: 46398 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.780 AC: 118568 AN: 151976 Hom.: 46431 Cov.: 31 AF XY: 0.787 AC XY: 58441 AN XY: 74296

African (AFR) AF: 0.733 AC: 30336 AN: 41400

American (AMR) AF: 0.808 AC: 12345 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3468

East Asian (EAS) AF: 0.876 AC: 4531 AN: 5172

South Asian (SAS) AF: 0.824 AC: 3968 AN: 4818

European-Finnish (FIN) AF: 0.841 AC: 8885 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53264 AN: 67958

Other (OTH) AF: 0.770 AC: 1624 AN: 2110

Alfa AF: 0.785 Hom.: 8181

Bravo AF: 0.774

Asia WGS AF: 0.858 AC: 2983 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		0.074
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: rs7800159; hg19: chr7-7401954;