rs17167055

Variant names:

• chr7-7376228-A-G
• rs17167055
• NM_001037763.3:c.2323-731T>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.2323-731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,066 control chromosomes in the GnomAD database, including 3,994 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 0.15 (3994 hom., cov: 32)
• Consequence: COL28A1 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.2323-731T>C		intron_variant	Intron 30 of 34	ENST00000399429.8	NP_001032852.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.2323-731T>C		intron_variant	Intron 30 of 34	1	NM_001037763.3	ENSP00000382356.3

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22562 AN: 151948 Hom.: 3979 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.149 AC: 22607 AN: 152066 Hom.: 3994 Cov.: 32 AF XY: 0.142 AC XY: 10589 AN XY: 74372

African (AFR) AF: 0.422 AC: 17481 AN: 41400

American (AMR) AF: 0.0715 AC: 1092 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0309 AC: 149 AN: 4828

European-Finnish (FIN) AF: 0.0158 AC: 168 AN: 10626

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0483 AC: 3286 AN: 67966

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.115 Hom.: 456

Bravo AF: 0.165

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.6
DANN	Benign	0.67
PhyloP100		1.4
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: rs17167055; hg19: chr7-7415859;