dbSNP rs1458201: CTF2P:n.30904808G>A (chr16-30904808-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.216 in 152,490 control chromosomes in the GnomAD database, including 4,405 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 0.22 ( 4399 hom., cov: 33)

Exomes 𝑓: 0.22 ( 6 hom. )

Consequence

CTF2P
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.391

Publications

12 publications found

Variant links:

Genes affected

CTF2P (HGNC:33173): (cardiotrophin 2, pseudogene) The cytokine neuropoietin belongs to the IL-6 superfamily. This gene has been inactivated by mutation and is nonfunctional in humans. [provided by RefSeq, Mar 2013]

CTF2P links:

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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=-0.64).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTF2P		n.30904808G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTF2P	ENST00000412003.1 link	n.154-10C>T		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32848

AN:

152082

Hom.:

4399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.0873

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.217

GnomAD4 exome

AF:

0.221

AC:

AN:

290

Hom.:

Cov.:

AF XY:

0.215

AC XY:

AN XY:

200

show subpopulations

African (AFR)

AF:

0.125

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.196

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.233

AC:

AN:

202

Other (OTH)

AF:

0.136

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

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:

0.216

AC:

32860

AN:

152200

Hom.:

4399

Cov.:

AF XY:

0.225

AC XY:

16738

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.102

AC:

4218

AN:

41536

American (AMR)

AF:

0.299

AC:

4577

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.175

AC:

607

AN:

3472

East Asian (EAS)

AF:

0.0870

AC:

451

AN:

5186

South Asian (SAS)

AF:

0.643

AC:

3102

AN:

4824

European-Finnish (FIN)

AF:

0.254

AC:

2694

AN:

10594

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16436

AN:

67978

Other (OTH)

AF:

0.222

AC:

469

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1268

2536

3803

5071

6339

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.217

Hom.:

4701

Bravo

AF:

0.203

Asia WGS

AF:

0.383

AC:

1328

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

5.4

(source)

DANN

Benign

0.81

PhyloP100

-0.39

Splicing

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