chr7-7359465-T-G

Position:

• chr7-7359465-T-G

Variant summary

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

The NM_001037763.3(COL28A1):​c.3206-660A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,008 control chromosomes in the GnomAD database, including 37,177 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 0.67 (37177 hom., cov: 31)
• Consequence: COL28A1 NM_001037763.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.3206-660A>C		intron_variant		ENST00000399429.8	NP_001032852.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.3206-660A>C		intron_variant		1	NM_001037763.3	ENSP00000382356.3
COL28A1	ENST00000453441.1	c.71-660A>C		intron_variant		2		ENSP00000391380.1
COL28A1	ENST00000430711.5	n.257-660A>C		intron_variant		5		ENSP00000413093.1

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101642 AN: 151890 Hom.: 37170 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.669 AC: 101689 AN: 152008 Hom.: 37177 Cov.: 31 AF XY: 0.679 AC XY: 50427 AN XY: 74312

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.770

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.688

Alfa AF: 0.718 Hom.: 6527

Bravo AF: 0.648

Asia WGS AF: 0.833 AC: 2895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.65

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: rs2159710; hg19: chr7-7399096;