7-7359773-C-T

Variant names:

• chr7-7359773-C-T
• rs10486158
• NM_001037763.3:c.3205+617G>A

Variant summary

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

The NM_001037763.3(COL28A1):​c.3205+617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,044 control chromosomes in the GnomAD database, including 36,454 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 0.65 (36454 hom., cov: 32)
• Consequence: COL28A1 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 10 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=-0.85).
• 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.3205+617G>A		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.3205+617G>A		intron	N/A	ENSP00000382356.3
	COL28A1	ENST00000453441.1	TSL:2	c.70+617G>A		intron	N/A	ENSP00000391380.1
	COL28A1	ENST00000430711.5	TSL:5	n.256+617G>A		intron	N/A	ENSP00000413093.1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99472 AN: 151926 Hom.: 36447 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.654 AC: 99507 AN: 152044 Hom.: 36454 Cov.: 32 AF XY: 0.665 AC XY: 49411 AN XY: 74334

African (AFR) AF: 0.296 AC: 12256 AN: 41444

American (AMR) AF: 0.766 AC: 11700 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2646 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4537 AN: 5180

South Asian (SAS) AF: 0.822 AC: 3966 AN: 4824

European-Finnish (FIN) AF: 0.840 AC: 8875 AN: 10560

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53133 AN: 67986

Other (OTH) AF: 0.679 AC: 1431 AN: 2108

Alfa AF: 0.716 Hom.: 67063

Bravo AF: 0.632

Asia WGS AF: 0.831 AC: 2885 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.92
DANN	Benign	0.74
PhyloP100		-1.3
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: rs10486158; hg19: chr7-7399404;