3-113361102-G-T

Variant names:

• chr3-113361102-G-T
• rs16860868
• NM_001164496.2:c.2934+2043C>A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS1

The NM_001164496.2(CFAP44):​c.2934+2043C>A variant causes a intron change. The variant allele was found at a frequency of 0.00104 in 207,766 control chromosomes in the GnomAD database, including 2 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 0.00092 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0014 (1 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)

SPICE1-CFAP44 (HGNC:58084):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00092 (140/152104) while in subpopulation EAS AF= 0.0099 (51/5154). AF 95% confidence interval is 0.00773. There are 1 homozygotes in gnomad4. There are 81 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP44	NM_001164496.2	c.2934+2043C>A		intron_variant	Intron 21 of 34	ENST00000393845.9	NP_001157968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP44	ENST00000393845.9	c.2934+2043C>A		intron_variant	Intron 21 of 34	5	NM_001164496.2	ENSP00000377428.2
RABGGTBP1	ENST00000462549.1	n.836G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
CFAP44	ENST00000490481.1	n.165+2043C>A		intron_variant	Intron 1 of 3	5		ENSP00000419269.1

Frequencies

GnomAD3 genomes AF: 0.000928 AC: 141 AN: 151986 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.0101

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00398

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000544

Gnomad OTH AF: 0.000957

GnomAD4 exome AF: 0.00138 AC: 77 AN: 55662 Hom.: 1 Cov.: 0 AF XY: 0.00110 AC XY: 35 AN XY: 31930

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000888

Gnomad4 EAS exome AF: 0.00433

Gnomad4 SAS exome AF: 0.000381

Gnomad4 FIN exome AF: 0.00384

Gnomad4 NFE exome AF: 0.000882

Gnomad4 OTH exome AF: 0.00311

GnomAD4 genome AF: 0.000920 AC: 140 AN: 152104 Hom.: 1 Cov.: 31 AF XY: 0.00109 AC XY: 81 AN XY: 74340

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.00990

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00398

Gnomad4 NFE AF: 0.000544

Gnomad4 OTH AF: 0.000947

Alfa AF: 0.00144 Hom.: 202

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	0.51

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;