Variant chr5-178247778-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_173465.4(COL23A1):c.1266G>A(p.Pro422=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00398 in 1,613,324 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0041 ( 25 hom. )

Consequence

COL23A1
NM_173465.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.167

Variant links:

Genes affected

COL23A1 (HGNC:22990): (collagen type XXIII alpha 1 chain) COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]

COL23A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 5-178247778-C-T is Benign according to our data. Variant chr5-178247778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656127.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.167 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL23A1	NM_173465.4 linkuse as main transcript	c.1266G>A	p.Pro422=	synonymous_variant	21/29	ENST00000390654.8	NP_775736.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL23A1	ENST00000390654.8 linkuse as main transcript	c.1266G>A	p.Pro422=	synonymous_variant	21/29	5	NM_173465.4	ENSP00000375069	P1	Q86Y22-1

Frequencies

GnomAD3 genomes

AF:

0.00291

AC:

443

AN:

152088

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00475

Gnomad OTH

AF:

0.00240

GnomAD3 exomes

AF:

0.00311

AC:

772

AN:

248226

Hom.:

AF XY:

0.00322

AC XY:

434

AN XY:

134864

show subpopulations

Gnomad AFR exome

AF:

0.000916

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.00220

Gnomad EAS exome

AF:

0.0000557

Gnomad SAS exome

AF:

0.00206

Gnomad FIN exome

AF:

0.000791

Gnomad NFE exome

AF:

0.00517

Gnomad OTH exome

AF:

0.00365

GnomAD4 exome

AF:

0.00409

AC:

5973

AN:

1461118

Hom.:

Cov.:

AF XY:

0.00407

AC XY:

2956

AN XY:

726880

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00150

Gnomad4 ASJ exome

AF:

0.00237

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00245

Gnomad4 FIN exome

AF:

0.000974

Gnomad4 NFE exome

AF:

0.00479

Gnomad4 OTH exome

AF:

0.00356

GnomAD4 genome

AF:

0.00291

AC:

443

AN:

152206

Hom.:

Cov.:

AF XY:

0.00266

AC XY:

198

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.00116

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00475

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00333

Hom.:

Bravo

AF:

0.00284

EpiCase

AF:

0.00578

EpiControl

AF:

0.00676

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

COL23A1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

7.2

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

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