dbSNP rs3838975: CFAP74:c.2176+18delG (chr1-1955672-GC-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001304360.2(CFAP74):c.2176+18delG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,612,216 control chromosomes in the GnomAD database, including 54,719 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 4067 hom., cov: 28)

Exomes 𝑓: 0.26 ( 50652 hom. )

Consequence

CFAP74
NM_001304360.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

Publications

7 publications found

Variant links:

Genes affected

CFAP74 (HGNC:29368): (cilia and flagella associated protein 74) Predicted to be involved in axoneme assembly. Predicted to be located in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

CFAP74 Gene-Disease associations (from GenCC):

ciliary dyskinesia, primary, 49, without situs inversus
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
primary ciliary dyskinesia
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

CFAP74 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304360.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP74	NM_001304360.2	MANE Select	c.2176+18delG		intron	N/A	NP_001291289.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CFAP74	ENST00000682832.2	MANE Select	c.2176+18delG	intron	N/A	ENSP00000508276.2
CFAP74	ENST00000468610.5	TSL:1	n.2209+18delG	intron	N/A
CFAP74	ENST00000270720.11	TSL:5	n.2350delG	non_coding_transcript_exon	Exon 18 of 18

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33381

AN:

151792

Hom.:

4068

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.217

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.225

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.222

GnomAD2 exomes

AF:

0.184

AC:

39879

AN:

216886

AF XY:

0.187

show subpopulations

Gnomad AFR exome

AF:

0.0848

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.128

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.217

Gnomad OTH exome

AF:

0.191

GnomAD4 exome

AF:

0.260

AC:

379999

AN:

1460304

Hom.:

50652

Cov.:

AF XY:

0.259

AC XY:

188265

AN XY:

726472

show subpopulations

African (AFR)

AF:

0.137

AC:

4581

AN:

33450

American (AMR)

AF:

0.236

AC:

10553

AN:

44680

Ashkenazi Jewish (ASJ)

AF:

0.257

AC:

6703

AN:

26084

East Asian (EAS)

AF:

0.260

AC:

10292

AN:

39598

South Asian (SAS)

AF:

0.190

AC:

16379

AN:

86236

European-Finnish (FIN)

AF:

0.225

AC:

11933

AN:

53130

Middle Eastern (MID)

AF:

0.254

AC:

1460

AN:

5754

European-Non Finnish (NFE)

AF:

0.273

AC:

303138

AN:

1111082

Other (OTH)

AF:

0.248

AC:

14960

AN:

60290

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

17218

34435

51653

68870

86088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10092

20184

30276

40368

50460

<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:

0.220

AC:

33376

AN:

151912

Hom.:

4067

Cov.:

AF XY:

0.216

AC XY:

16024

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.140

AC:

5813

AN:

41462

American (AMR)

AF:

0.217

AC:

3314

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

881

AN:

3466

East Asian (EAS)

AF:

0.210

AC:

1074

AN:

5126

South Asian (SAS)

AF:

0.182

AC:

877

AN:

4816

European-Finnish (FIN)

AF:

0.225

AC:

2372

AN:

10532

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.269

AC:

18272

AN:

67912

Other (OTH)

AF:

0.219

AC:

463

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

1123

2246

3369

4492

5615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.130

Hom.:

438

Asia WGS

AF:

0.183

AC:

638

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.088

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