7-7363384-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001037763.3(COL28A1):c.3067-2856A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,118 control chromosomes in the GnomAD database, including 41,237 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 0.73 (41237 hom., cov: 32)
• Consequence: COL28A1 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL28A1	NM_001037763.3	c.3067-2856A>G		intron_variant		ENST00000399429.8
LOC107986764	XR_002956539.2	n.442-13177T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL28A1	ENST00000399429.8	c.3067-2856A>G		intron_variant		1	NM_001037763.3	P1
COL28A1	ENST00000430711.5	c.118-2856A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110853 AN: 152000 Hom.: 41208 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.729 AC: 110937 AN: 152118 Hom.: 41237 Cov.: 32 AF XY: 0.735 AC XY: 54671 AN XY: 74358

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.731

Alfa AF: 0.760 Hom.: 21833

Bravo AF: 0.720

Asia WGS AF: 0.842 AC: 2926 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.9
Dann	Benign	0.62

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: rs4724977; hg19: chr7-7403015;