Genetic Variant CTXN3:c.*463T>C (chr5-127658230-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001048252.3(CTXN3):c.*463T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 174,066 control chromosomes in the GnomAD database, including 9,800 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8359 hom., cov: 32)

Exomes 𝑓: 0.35 ( 1441 hom. )

Consequence

CTXN3
NM_001048252.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Publications

7 publications found

Variant links:

Genes affected

CTXN3 (HGNC:31110): (cortexin 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CTXN3 links:

ENSG00000248799 (HGNC:):

ENSG00000248799 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CTXN3	NM_001048252.3 link	c.*463T>C	3_prime_UTR_variant	Exon 3 of 3	ENST00000379445.8	NP_001041717.1	Q4LDR2
CTXN3	NM_001127385.2 link	c.*463T>C	3_prime_UTR_variant	Exon 3 of 3		NP_001120857.1	Q4LDR2
LOC105379164	XR_002956226.1 link	n.139+5394A>G	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTXN3	ENST00000379445.8 link	c.*463T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_001048252.3	ENSP00000368758.3		Q4LDR2

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47752

AN:

151988

Hom.:

8357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.315

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.341

GnomAD4 exome

AF:

0.346

AC:

7592

AN:

21960

Hom.:

1441

Cov.:

AF XY:

0.343

AC XY:

3736

AN XY:

10878

show subpopulations

African (AFR)

AF:

0.150

AC:

AN:

American (AMR)

AF:

0.240

AC:

316

AN:

1314

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

AN:

East Asian (EAS)

AF:

0.228

AC:

AN:

312

South Asian (SAS)

AF:

0.270

AC:

185

AN:

684

European-Finnish (FIN)

AF:

0.349

AC:

5175

AN:

14814

Middle Eastern (MID)

AF:

0.429

AC:

AN:

European-Non Finnish (NFE)

AF:

0.385

AC:

1662

AN:

4320

Other (OTH)

AF:

0.382

AC:

152

AN:

398

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

258

516

775

1033

1291

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

104

130

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.314

AC:

47753

AN:

152106

Hom.:

8359

Cov.:

AF XY:

0.308

AC XY:

22909

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.176

AC:

7312

AN:

41526

American (AMR)

AF:

0.297

AC:

4539

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.409

AC:

1420

AN:

3468

East Asian (EAS)

AF:

0.242

AC:

1248

AN:

5166

South Asian (SAS)

AF:

0.244

AC:

1173

AN:

4814

European-Finnish (FIN)

AF:

0.360

AC:

3807

AN:

10580

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.399

AC:

27133

AN:

67950

Other (OTH)

AF:

0.336

AC:

710

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1638

3276

4914

6552

8190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.335

Hom.:

4916

Bravo

AF:

0.302

Asia WGS

AF:

0.208

AC:

726

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.8

(source)

DANN

Benign

0.72

PhyloP100

-0.010

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over