Genetic Variant CCDC144NL:n.390G>A (chr17-20895774-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000327925.7(CCDC144NL):n.390G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00731 in 1,613,506 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0052 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0075 ( 44 hom. )

Consequence

CCDC144NL
ENST00000327925.7 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.121

Publications

4 publications found

Variant links:

Genes affected

CCDC144NL (HGNC:):

CCDC144NL links:

CCDC144NL-AS1 (HGNC:51340): (CCDC144NL antisense RNA 1)

CCDC144NL-AS1 links:

CCDC144NL (HGNC:33735): (CCDC144A N-terminal like (pseudogene))

CCDC144NL links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007117778).

BP6

Variant 17-20895774-C-T is Benign according to our data. Variant chr17-20895774-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2647571.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000327925.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
CCDC144NL	NR_164128.1	n.390G>A	non_coding_transcript_exon	Exon 1 of 4
CCDC144NL-AS1	NR_104185.2	n.362+3342C>T	intron	N/A
CCDC144NL-AS1	NR_160710.1	n.620+3342C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CCDC144NL	ENST00000327925.7	TSL:1	n.390G>A	non_coding_transcript_exon	Exon 1 of 4
CCDC144NL-AS1	ENST00000583962.3	TSL:1	n.424+3342C>T	intron	N/A
CCDC144NL	ENST00000647562.3		n.247G>A	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00524

AC:

797

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00616

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00476

Gnomad FIN

AF:

0.00677

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00780

Gnomad OTH

AF:

0.00335

GnomAD2 exomes

AF:

0.00489

AC:

1226

AN:

250756

AF XY:

0.00514

show subpopulations

Gnomad AFR exome

AF:

0.00131

Gnomad AMR exome

AF:

0.00234

Gnomad ASJ exome

AF:

0.000794

Gnomad EAS exome

AF:

0.000109

Gnomad FIN exome

AF:

0.00596

Gnomad NFE exome

AF:

0.00753

Gnomad OTH exome

AF:

0.00311

GnomAD4 exome

AF:

0.00753

AC:

10999

AN:

1461234

Hom.:

Cov.:

AF XY:

0.00744

AC XY:

5407

AN XY:

726936

show subpopulations

African (AFR)

AF:

0.00126

AC:

AN:

33450

American (AMR)

AF:

0.00226

AC:

101

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.000804

AC:

AN:

26132

East Asian (EAS)

AF:

0.000202

AC:

AN:

39698

South Asian (SAS)

AF:

0.00391

AC:

337

AN:

86226

European-Finnish (FIN)

AF:

0.00627

AC:

335

AN:

53404

Middle Eastern (MID)

AF:

0.00201

AC:

AN:

5464

European-Non Finnish (NFE)

AF:

0.00880

AC:

9788

AN:

1111810

Other (OTH)

AF:

0.00590

AC:

356

AN:

60334

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

489

978

1466

1955

2444

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

374

748

1122

1496

1870

<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:

0.00524

AC:

798

AN:

152272

Hom.:

Cov.:

AF XY:

0.00518

AC XY:

386

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.00154

AC:

AN:

41532

American (AMR)

AF:

0.00621

AC:

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3472

East Asian (EAS)

AF:

0.000387

AC:

AN:

5172

South Asian (SAS)

AF:

0.00477

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00677

AC:

AN:

10632

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00781

AC:

531

AN:

68028

Other (OTH)

AF:

0.00331

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

124

165

206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00658

Hom.:

Bravo

AF:

0.00487

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.00886

AC:

ExAC

AF:

0.00460

AC:

559

EpiCase

AF:

0.00720

EpiControl

AF:

0.00741

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.71

CADD

Benign

4.1

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.0016

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0092

LIST_S2

Benign

0.63

M_CAP

Benign

0.0017

MetaRNN

Benign

0.0071

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.22

PhyloP100

-0.12

PrimateAI

Uncertain

0.54

Polyphen

0.33

ClinPred

0.0016

GERP RS

-1.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.036

gMVP

0.14

Mutation Taster

=100/0

polymorphism

(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