rs17167055

Positions:

• chr7-7376228-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.2323-731T>C		intron_variant		ENST00000399429.8	NP_001032852.2
LOC107986764	XR_002956539.2	n.442-333A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.2323-731T>C		intron_variant		1	NM_001037763.3	ENSP00000382356	P1

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

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.0715

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.0483

Gnomad4 OTH AF: 0.130

Alfa AF: 0.106 Hom.: 392

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

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: rs17167055; hg19: chr7-7415859;