rs17168526

Variant names:

• chr7-7531789-T-C
• rs17168526
• NM_001037763.3:c.240A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-7531789-T-C
• chr7-7531789-T-G

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BA1

The NM_001037763.3(COL28A1):​c.240A>G​(p.Gln80Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00426 in 1,605,212 control chromosomes in the GnomAD database, including 243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.022 (146 hom., cov: 32)
  • Exomes 𝑓: 0.0024 (97 hom.)
• Consequence: COL28A1 NM_001037763.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.93
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 7-7531789-T-C is Benign according to our data. Variant chr7-7531789-T-C is described in ClinVar as Benign. ClinVar VariationId is 776205.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.93 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001037763.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL28A1	NM_001037763.3	MANE Select	c.240A>G	p.Gln80Gln	synonymous	Exon 3 of 35	NP_001032852.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COL28A1	ENST00000399429.8	TSL:1 MANE Select	c.240A>G	p.Gln80Gln	synonymous	Exon 3 of 35	ENSP00000382356.3

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 3329 AN: 152186 Hom.: 147 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00779

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0143

GnomAD2 exomes AF: 0.00573 AC: 1426 AN: 248946 AF XY: 0.00455

Gnomad AFR exome AF: 0.0785

Gnomad AMR exome AF: 0.00411

Gnomad ASJ exome AF: 0.000299

Gnomad EAS exome AF: 0.000111

Gnomad FIN exome AF: 0.000186

Gnomad NFE exome AF: 0.000293

Gnomad OTH exome AF: 0.00248

GnomAD4 exome AF: 0.00240 AC: 3494 AN: 1452906 Hom.: 97 Cov.: 27 AF XY: 0.00211 AC XY: 1524 AN XY: 723584

African (AFR) AF: 0.0783 AC: 2601 AN: 33236

American (AMR) AF: 0.00467 AC: 209 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.000422 AC: 11 AN: 26062

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39646

South Asian (SAS) AF: 0.000314 AC: 27 AN: 86090

European-Finnish (FIN) AF: 0.000131 AC: 7 AN: 53416

Middle Eastern (MID) AF: 0.00729 AC: 42 AN: 5760

European-Non Finnish (NFE) AF: 0.000251 AC: 277 AN: 1103876

Other (OTH) AF: 0.00526 AC: 316 AN: 60108

GnomAD4 genome AF: 0.0219 AC: 3338 AN: 152306 Hom.: 146 Cov.: 32 AF XY: 0.0217 AC XY: 1616 AN XY: 74498

African (AFR) AF: 0.0761 AC: 3163 AN: 41548

American (AMR) AF: 0.00778 AC: 119 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4830

European-Finnish (FIN) AF: 0.0000941 AC: 1 AN: 10628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 68028

Other (OTH) AF: 0.0142 AC: 30 AN: 2116

Alfa AF: 0.00785 Hom.: 136

Bravo AF: 0.0244

Asia WGS AF: 0.00722 AC: 25 AN: 3478

EpiCase AF: 0.000545

EpiControl AF: 0.000178

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jul 25, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.15
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs17168526; hg19: chr7-7571420;