7-7359465-T-G

Variant names:

• chr7-7359465-T-G
• rs2159710
• NM_001037763.3:c.3206-660A>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.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
• Publications: 2 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=-0.86).
• 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 rank	MANE	Protein	UniProt
COL28A1	NM_001037763.3	c.3206-660A>C		intron_variant	Intron 34 of 34	ENST00000399429.8	NP_001032852.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8	c.3206-660A>C		intron_variant	Intron 34 of 34	1	NM_001037763.3	ENSP00000382356.3
COL28A1	ENST00000453441.1	c.71-660A>C		intron_variant	Intron 1 of 2	2		ENSP00000391380.1
COL28A1	ENST00000430711.5	n.257-660A>C		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.347 AC: 14363 AN: 41420

American (AMR) AF: 0.770 AC: 11759 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2645 AN: 3468

East Asian (EAS) AF: 0.876 AC: 4534 AN: 5176

South Asian (SAS) AF: 0.822 AC: 3963 AN: 4820

European-Finnish (FIN) AF: 0.841 AC: 8882 AN: 10566

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

European-Non Finnish (NFE) AF: 0.782 AC: 53125 AN: 67970

Other (OTH) AF: 0.688 AC: 1452 AN: 2110

Alfa AF: 0.706 Hom.: 6571

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
PhyloP100		1.6
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: rs2159710; hg19: chr7-7399096;