Variant chr7-7373261-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001037763.3(COL28A1):c.2645A>T(p.Gln882Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00394 in 1,614,184 control chromosomes in the GnomAD database, including 242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.022 ( 140 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 102 hom. )

Consequence

COL28A1
NM_001037763.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.13

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:

LOC107986764 (HGNC:):

LOC107986764 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002996266).

BP6

Variant 7-7373261-T-A is Benign according to our data. Variant chr7-7373261-T-A is described in ClinVar as [Benign]. Clinvar id is 776204.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL28A1	NM_001037763.3 linkuse as main transcript	c.2645A>T	p.Gln882Leu	missense_variant	32/35	ENST00000399429.8	NP_001032852.2
LOC107986764	XR_002956539.2 linkuse as main transcript	n.442-3300T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL28A1	ENST00000399429.8 linkuse as main transcript	c.2645A>T	p.Gln882Leu	missense_variant	32/35	1	NM_001037763.3	ENSP00000382356	P1	Q2UY09-1

Frequencies

GnomAD3 genomes

AF:

0.0216

AC:

3286

AN:

152172

Hom.:

140

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0758

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00628

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000265

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.00527

AC:

1316

AN:

249526

Hom.:

AF XY:

0.00403

AC XY:

545

AN XY:

135376

show subpopulations

Gnomad AFR exome

AF:

0.0750

Gnomad AMR exome

AF:

0.00313

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.0000654

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.000221

Gnomad OTH exome

AF:

0.00281

GnomAD4 exome

AF:

0.00210

AC:

3076

AN:

1461894

Hom.:

102

Cov.:

AF XY:

0.00180

AC XY:

1308

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.0747

Gnomad4 AMR exome

AF:

0.00380

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000944

Gnomad4 OTH exome

AF:

0.00445

GnomAD4 genome

AF:

0.0216

AC:

3290

AN:

152290

Hom.:

140

Cov.:

AF XY:

0.0204

AC XY:

1519

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0758

Gnomad4 AMR

AF:

0.00621

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000265

Gnomad4 OTH

AF:

0.0132

Alfa

AF:

0.00325

Hom.:

Bravo

AF:

0.0232

ESP6500AA

AF:

0.0659

AC:

266

ESP6500EA

AF:

0.000239

AC:

ExAC

AF:

0.00651

AC:

787

Asia WGS

AF:

0.00433

AC:

AN:

3478

EpiCase

AF:

0.000109

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 25, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.038

Eigen

Benign

-0.13

Eigen_PC

Benign

-0.0034

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.59

MetaRNN

Benign

0.0030

MetaSVM

Benign

-0.83

MutationAssessor

Benign

1.7

MutationTaster

Benign

0.73

PrimateAI

Benign

0.31

PROVEAN

Uncertain

-2.5

REVEL

Uncertain

0.31

Sift

Benign

0.12

Sift4G

Uncertain

0.035

Polyphen

0.10

Vest4

0.35

MVP

0.41

MPC

0.031

ClinPred

0.027

GERP RS

4.3

Varity_R

0.18

gMVP

0.53

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

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