rs16860868

chr3-113361102-G-Cchr3-113361102-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164496.2(CFAP44):c.2934+2043C>G variant causes a intron change. The variant allele was found at a frequency of 0.195 in 207,524 control chromosomes in the GnomAD database, including 4,697 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 0.18 (3121 hom., cov: 31)
  • Exomes 𝑓: 0.22 (1576 hom.)
• Consequence: CFAP44 NM_001164496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.47

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]

RABGGTBP1 (HGNC:56479): (RABGGTB pseudogene 1)

LOC127898559 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP44	NM_001164496.2	c.2934+2043C>G		intron_variant		ENST00000393845.9
LOC127898559	NR_183046.1	n.5748+2043C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP44	ENST00000393845.9	c.2934+2043C>G		intron_variant		5	NM_001164496.2	P2
RABGGTBP1	ENST00000462549.1	n.836G>C		non_coding_transcript_exon_variant	1/1
CFAP44	ENST00000490481.1	c.166+2043C>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28125 AN: 151950 Hom.: 3120 Cov.: 31

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.223 AC: 12345 AN: 55456 Hom.: 1576 Cov.: 0 AF XY: 0.225 AC XY: 7174 AN XY: 31822

Gnomad4 AFR exome AF: 0.0570

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.171

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.265

Gnomad4 FIN exome AF: 0.312

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.185 AC: 28122 AN: 152068 Hom.: 3121 Cov.: 31 AF XY: 0.194 AC XY: 14443 AN XY: 74322

Gnomad4 AFR AF: 0.0812

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.179

Alfa AF: 0.112 Hom.: 202

Bravo AF: 0.169

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	5.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16860868; hg19: chr3-113079949;