Variant X-110681487-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001143981.2(CHRDL1):c.1151G>A(p.Arg384Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000704 in 1,205,073 control chromosomes in the GnomAD database, including 4 homozygotes. There are 237 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 2 hom., 124 hem., cov: 23)

Exomes 𝑓: 0.00038 ( 2 hom. 113 hem. )

Consequence

CHRDL1
NM_001143981.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.575

Variant links:

Genes affected

CHRDL1 (HGNC:29861): (chordin like 1) This gene encodes an antagonist of bone morphogenetic protein 4. The encoded protein may play a role in topographic retinotectal projection and in the regulation of retinal angiogenesis in response to hypoxia. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]

CHRDL1 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=0.006048888).

BP6

Variant X-110681487-C-T is Benign according to our data. Variant chrX-110681487-C-T is described in ClinVar as [Benign]. Clinvar id is 777821.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-110681487-C-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00382 (428/112062) while in subpopulation AFR AF= 0.0114 (353/30861). AF 95% confidence interval is 0.0105. There are 2 homozygotes in gnomad4. There are 124 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Homozygotes in GnomAd at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRDL1	NM_001143981.2 linkuse as main transcript	c.1151G>A	p.Arg384Gln	missense_variant	10/12	ENST00000372042.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRDL1	ENST00000372042.6 linkuse as main transcript	c.1151G>A	p.Arg384Gln	missense_variant	10/12	2	NM_001143981.2	A1	Q9BU40-4

Frequencies

GnomAD3 genomes

AF:

0.00382

AC:

428

AN:

112009

Hom.:

Cov.:

AF XY:

0.00363

AC XY:

124

AN XY:

34171

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00596

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00840

Gnomad NFE

AF:

0.0000376

Gnomad OTH

AF:

0.00535

GnomAD3 exomes

AF:

0.00113

AC:

202

AN:

179021

Hom.:

AF XY:

0.000784

AC XY:

AN XY:

63739

show subpopulations

Gnomad AFR exome

AF:

0.0112

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000735

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000496

Gnomad OTH exome

AF:

0.00135

GnomAD4 exome

AF:

0.000384

AC:

420

AN:

1093011

Hom.:

Cov.:

AF XY:

0.000315

AC XY:

113

AN XY:

358675

show subpopulations

Gnomad4 AFR exome

AF:

0.00966

Gnomad4 AMR exome

AF:

0.00190

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.0000188

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000620

Gnomad4 OTH exome

AF:

0.000958

GnomAD4 genome

AF:

0.00382

AC:

428

AN:

112062

Hom.:

Cov.:

AF XY:

0.00362

AC XY:

124

AN XY:

34234

show subpopulations

Gnomad4 AFR

AF:

0.0114

Gnomad4 AMR

AF:

0.00595

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000376

Gnomad4 OTH

AF:

0.00528

Alfa

AF:

0.00173

Hom.:

Bravo

AF:

0.00477

ESP6500AA

AF:

0.0107

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00110

AC:

133

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

Invitae

Sep 19, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.77

Cadd

Benign

Dann

Benign

0.96

DEOGEN2

Benign

0.085

T;.;.;.;.

FATHMM_MKL

Benign

0.60

LIST_S2

Uncertain

0.86

D;D;D;D;D

MetaRNN

Benign

0.0060

T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

L;.;.;.;.

MutationTaster

Benign

0.99

N;N;N;N;N;N;N

PrimateAI

Benign

0.36

PROVEAN

Benign

0.45

N;N;N;N;N

REVEL

Benign

0.026

Sift

Benign

0.11

T;T;T;T;T

Sift4G

Benign

0.14

T;T;T;T;T

Polyphen

0.0010

B;.;.;.;.

Vest4

0.13

MVP

0.33

MPC

0.39

ClinPred

0.021

GERP RS

2.2

Varity_R

0.056

gMVP

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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