dbSNP rs13064411: CFAP44:p.Asp1381Asp (chr3-113327793-A-G) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP7BA1

The NM_001164496.2(CFAP44):c.4143T>C(p.Asp1381Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,536,600 control chromosomes in the GnomAD database, including 15,072 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 966 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14106 hom. )

Consequence

CFAP44
NM_001164496.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.24

Publications

17 publications found

Variant links:

Genes affected

CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Apr 2022]

CFAP44 Gene-Disease associations (from GenCC):

spermatogenic failure 20
Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
non-syndromic male infertility due to sperm motility disorder
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CFAP44 links:

SPICE1-CFAP44 (HGNC:58084):

SPICE1-CFAP44 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP7

Synonymous conserved (PhyloP=2.24 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP44	NM_001164496.2 link	c.4143T>C	p.Asp1381Asp	synonymous_variant	Exon 27 of 35	ENST00000393845.9	NP_001157968.1	Q96MT7-2Q9NUU0Q9UF55

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9 link	c.4143T>C	p.Asp1381Asp	synonymous_variant	Exon 27 of 35	5	NM_001164496.2	ENSP00000377428.2		Q96MT7-2
CFAP44	ENST00000461734.1 link	n.3T>C		non_coding_transcript_exon_variant	Exon 1 of 10	2		ENSP00000418795.1		H0Y896

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15305

AN:

152138

Hom.:

966

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0265

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.0829

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0742

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.116

AC:

16703

AN:

144160

AF XY:

0.119

show subpopulations

Gnomad AFR exome

AF:

0.0270

Gnomad AMR exome

AF:

0.0634

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.0806

Gnomad NFE exome

AF:

0.148

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.139

AC:

192513

AN:

1384344

Hom.:

14106

Cov.:

AF XY:

0.139

AC XY:

94742

AN XY:

683094

show subpopulations

African (AFR)

AF:

0.0231

AC:

731

AN:

31584

American (AMR)

AF:

0.0686

AC:

2448

AN:

35698

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

4124

AN:

25168

East Asian (EAS)

AF:

0.0878

AC:

3134

AN:

35706

South Asian (SAS)

AF:

0.116

AC:

9182

AN:

79198

European-Finnish (FIN)

AF:

0.0873

AC:

3056

AN:

34994

Middle Eastern (MID)

AF:

0.114

AC:

648

AN:

5678

European-Non Finnish (NFE)

AF:

0.150

AC:

161681

AN:

1078430

Other (OTH)

AF:

0.130

AC:

7509

AN:

57888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

8059

16118

24178

32237

40296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5812

11624

17436

23248

29060

<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:

0.101

AC:

15307

AN:

152256

Hom.:

966

Cov.:

AF XY:

0.0977

AC XY:

7271

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0264

AC:

1098

AN:

41592

American (AMR)

AF:

0.0828

AC:

1265

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

548

AN:

3470

East Asian (EAS)

AF:

0.102

AC:

527

AN:

5182

South Asian (SAS)

AF:

0.111

AC:

536

AN:

4820

European-Finnish (FIN)

AF:

0.0742

AC:

788

AN:

10614

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10147

AN:

67978

Other (OTH)

AF:

0.0991

AC:

209

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

704

1409

2113

2818

3522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.136

Hom.:

4308

Bravo

AF:

0.0990

Asia WGS

AF:

0.0790

AC:

272

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

6.8

(source)

DANN

Benign

0.60

PhyloP100

2.2

Mutation Taster

=295/5

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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