rs13064411

Variant names:

• chr3-113327793-A-G
• rs13064411
• NM_001164496.2:c.4143T>C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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. 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 0.10 (966 hom., cov: 32)
  • Exomes 𝑓: 0.14 (14106 hom.)
• Consequence: CFAP44 NM_001164496.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

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]

SPICE1-CFAP44 (HGNC:58084):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• 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	c.4143T>C	p.Asp1381Asp	synonymous_variant	Exon 27 of 35	ENST00000393845.9	NP_001157968.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15305 AN: 152138 Hom.: 966 Cov.: 32

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

GnomAD3 exomes AF: 0.116 AC: 16703 AN: 144160 Hom.: 1141 AF XY: 0.119 AC XY: 9182 AN XY: 76988

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 SAS exome AF: 0.116

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.: 32 AF XY: 0.139 AC XY: 94742 AN XY: 683094

Gnomad4 AFR exome AF: 0.0231

Gnomad4 AMR exome AF: 0.0686

Gnomad4 ASJ exome AF: 0.164

Gnomad4 EAS exome AF: 0.0878

Gnomad4 SAS exome AF: 0.116

Gnomad4 FIN exome AF: 0.0873

Gnomad4 NFE exome AF: 0.150

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.101 AC: 15307 AN: 152256 Hom.: 966 Cov.: 32 AF XY: 0.0977 AC XY: 7271 AN XY: 74442

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.0828

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0742

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.0991

Alfa AF: 0.140 Hom.: 1984

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
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13064411; hg19: chr3-113046640;