dbSNP rs17168526: COL28A1:p.Gln80Gln (chr7-7531789-T-C) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.93

Variant links:

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]

COL28A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL28A1	NM_001037763.3 link	c.240A>G	p.Gln80Gln	synonymous_variant	Exon 3 of 35	ENST00000399429.8	NP_001032852.2	Q2UY09-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8 link	c.240A>G	p.Gln80Gln	synonymous_variant	Exon 3 of 35	1	NM_001037763.3	ENSP00000382356.3		Q2UY09-1

Frequencies

GnomAD3 genomes

AF:

0.0219

AC:

3329

AN:

152186

Hom.:

147

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.00573

AC:

1426

AN:

248946

Hom.:

AF XY:

0.00455

AC XY:

614

AN XY:

135046

show subpopulations

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 SAS exome

AF:

0.000392

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.:

Cov.:

AF XY:

0.00211

AC XY:

1524

AN XY:

723584

show subpopulations

Gnomad4 AFR exome

AF:

0.0783

Gnomad4 AMR exome

AF:

0.00467

Gnomad4 ASJ exome

AF:

0.000422

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.000314

Gnomad4 FIN exome

AF:

0.000131

Gnomad4 NFE exome

AF:

0.000251

Gnomad4 OTH exome

AF:

0.00526

GnomAD4 genome

AF:

0.0219

AC:

3338

AN:

152306

Hom.:

146

Cov.:

AF XY:

0.0217

AC XY:

1616

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.0761

Gnomad4 AMR

AF:

0.00778

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.000309

Gnomad4 OTH

AF:

0.0142

Alfa

AF:

0.00331

Hom.:

Bravo

AF:

0.0244

Asia WGS

AF:

0.00722

AC:

AN:

3478

EpiCase

AF:

0.000545

EpiControl

AF:

0.000178

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.12

DANN

Benign

0.15

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over