Genetic Variant CTF1:c.*766T>C (chr16-30903305-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_001330.5(CTF1):c.*766T>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 0.617 in 153,024 control chromosomes in the GnomAD database, including 29,789 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 0.62 ( 29557 hom., cov: 30)

Exomes 𝑓: 0.59 ( 232 hom. )

Consequence

CTF1
NM_001330.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.773

Publications

44 publications found

Variant links:

Genes affected

CTF1 (HGNC:2499): (cardiotrophin 1) The protein encoded by this gene is a secreted cytokine that induces cardiac myocyte hypertrophy in vitro. It has been shown to bind and activate the ILST/gp130 receoptor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

CTF1 Gene-Disease associations (from GenCC):

dilated cardiomyopathy
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

CTF1 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CTF1	NM_001330.5	MANE Select	c.*766T>C	3_prime_UTR	Exon 3 of 3	NP_001321.1
CTF1	NR_165660.1		n.1510T>C	non_coding_transcript_exon	Exon 3 of 3
CTF1	NM_001142544.3		c.*766T>C	3_prime_UTR	Exon 3 of 3	NP_001136016.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CTF1	ENST00000279804.3	TSL:1 MANE Select	c.*766T>C		3_prime_UTR	Exon 3 of 3	ENSP00000279804.2
	CTF1	ENST00000395019.3	TSL:1	c.*766T>C		3_prime_UTR	Exon 3 of 3	ENSP00000378465.3

Frequencies

GnomAD3 genomes

AF:

0.618

AC:

93705

AN:

151686

Hom.:

29538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.548

Gnomad AMI

AF:

0.678

Gnomad AMR

AF:

0.607

Gnomad ASJ

AF:

0.709

Gnomad EAS

AF:

0.907

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.675

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.645

Gnomad OTH

AF:

0.658

GnomAD4 exome

AF:

0.591

AC:

721

AN:

1220

Hom.:

232

Cov.:

AF XY:

0.578

AC XY:

517

AN XY:

894

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.611

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.335

AC:

AN:

260

European-Finnish (FIN)

AF:

0.583

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.665

AC:

480

AN:

722

Other (OTH)

AF:

0.636

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.618

AC:

93768

AN:

151804

Hom.:

29557

Cov.:

AF XY:

0.615

AC XY:

45580

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.548

AC:

22693

AN:

41382

American (AMR)

AF:

0.607

AC:

9250

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.709

AC:

2454

AN:

3462

East Asian (EAS)

AF:

0.907

AC:

4673

AN:

5152

South Asian (SAS)

AF:

0.319

AC:

1532

AN:

4804

European-Finnish (FIN)

AF:

0.675

AC:

7126

AN:

10552

Middle Eastern (MID)

AF:

0.769

AC:

226

AN:

294

European-Non Finnish (NFE)

AF:

0.645

AC:

43822

AN:

67900

Other (OTH)

AF:

0.654

AC:

1376

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1801

3603

5404

7206

9007

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<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:

0.643

Hom.:

36830

Bravo

AF:

0.620

Asia WGS

AF:

0.572

AC:

1995

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.0

(source)

DANN

Benign

0.56

PhyloP100

-0.77

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over