rs1262272674

Positions:

• chr3-113344603-G-A
• chr3-113344603-G-C

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001164496.2(CFAP44):​c.3175C>T​(p.Arg1059Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000794 in 1,384,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000079 (0 hom.)
• Consequence: CFAP44 NM_001164496.2 stop_gained
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.160

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]

LOC127898559 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-113344603-G-A is Pathogenic according to our data. Variant chr3-113344603-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 523153.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-113344603-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP44	NM_001164496.2	c.3175C>T	p.Arg1059Ter	stop_gained	23/35	ENST00000393845.9	NP_001157968.1
LOC127898559	NR_183046.1	n.5989C>T		non_coding_transcript_exon_variant	37/48

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9	c.3175C>T	p.Arg1059Ter	stop_gained	23/35	5	NM_001164496.2	ENSP00000377428	P2
CFAP44	ENST00000490481.1	c.298-2685C>T		intron_variant, NMD_transcript_variant		5		ENSP00000419269

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000794 AC: 11 AN: 1384778 Hom.: 0 Cov.: 31 AF XY: 0.00000732 AC XY: 5 AN XY: 683298

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000126

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000834

Gnomad4 OTH exome AF: 0.0000173

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Spermatogenic failure 20 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 02, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.34	D
BayesDel_noAF	Pathogenic	0.25
CADD	Pathogenic	34
DANN	Uncertain	0.99
Eigen	Uncertain	0.21
Eigen_PC	Benign	-0.16
FATHMM_MKL	Benign	0.028	N
MutationTaster	Benign	1.0	A
Vest4		0.051
ClinPred		0.70	D
GERP RS		1.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1262272674; hg19: chr3-113063450;